static char rcsid[] = "$Id: genome.c 207383 2017-06-15 20:58:03Z twu $"; #ifdef HAVE_CONFIG_H #include #endif #ifndef HAVE_MEMCPY # define memcpy(d,s,n) bcopy((s),(d),(n)) #endif #ifndef HAVE_MEMMOVE # define memmove(d,s,n) bcopy((s),(d),(n)) #endif #include "genome.h" #include #include #include #include #include /* For munmap */ #ifdef HAVE_UNISTD_H #include /* For lseek and close */ #endif #ifdef HAVE_SYS_TYPES_H #include /* For off_t */ #endif #ifdef HAVE_PTHREAD #include /* sys/types.h already included above */ #endif #include "assert.h" #include "except.h" #include "mem.h" #include "complement.h" #include "interval.h" #include "genomicpos.h" /* For Genomicpos_commafmt */ #include "types.h" #ifdef WORDS_BIGENDIAN #include "bigendian.h" #else #include "littleendian.h" #endif /* Uses 'A' instead of 'N' just as Oligoindex_hr_tally would do */ /* #define EXTRACT_GENOMICSEG 1 */ #ifdef DEBUG #define debug(x) x #else #define debug(x) #endif /* Print genomic segment */ #ifdef DEBUG1 #define debug1(x) x #else #define debug1(x) #endif /* Patching with strain information */ #ifdef DEBUG2 #define debug2(x) x #else #define debug2(x) #endif /* Nucleotides */ #ifdef DEBUG3 #define debug3(x) x #else #define debug3(x) #endif #define T Genome_T struct T { Access_T access; /* For either chars or blocks, whichever is used */ int chars_shmid; key_t chars_key; int blocks_shmid; key_t blocks_key; int fd; size_t len; char *chars; Genomecomp_T *blocks; bool compressedp; char *ptr; unsigned int left; #ifdef HAVE_PTHREAD pthread_mutex_t read_mutex; #endif }; Genomecomp_T * Genome_blocks (T this) { return this->blocks; } Univcoord_T Genome_totallength (T this) { if (this->compressedp == false) { return (Univcoord_T) this->len; } else { return (Univcoord_T) ((this->len/3) * 8); } } void Genome_free (T *old) { if (*old) { if ((*old)->access == ALLOCATED_PRIVATE) { if ((*old)->compressedp == true) { FREE((*old)->blocks); } else { FREE((*old)->chars); } } else if ((*old)->access == ALLOCATED_SHARED) { if ((*old)->compressedp == true) { Access_deallocate((*old)->blocks,(*old)->blocks_shmid,(*old)->blocks_key); } else { Access_deallocate((*old)->chars,(*old)->chars_shmid,(*old)->chars_key); } #ifdef HAVE_MMAP } else if ((*old)->access == MMAPPED) { if ((*old)->compressedp == true) { munmap((void *) (*old)->blocks,(*old)->len); } else { munmap((void *) (*old)->chars,(*old)->len); } close((*old)->fd); #endif } else if ((*old)->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_destroy(&(*old)->read_mutex); #endif close((*old)->fd); } FREE(*old); } return; } #if 0 void Genome_shmem_remove (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T genometype, bool genome_lc_p) { char *filename; bool compressedp = !genome_lc_p; if (compressedp == true) { if (genometype == GENOME_OLIGOS) { if (snps_root != NULL) { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char)); sprintf(filename,"%s/%s.genomecomp.%s",genomesubdir,fileroot,snps_root); } else { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomecomp")+1,sizeof(char)); sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot); } } else if (genometype == GENOME_BITS) { if (snps_root != NULL) { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char)); sprintf(filename,"%s/%s.genomebits128.%s",genomesubdir,fileroot,snps_root); } else { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomebits128")+1,sizeof(char)); sprintf(filename,"%s/%s.genomebits128",genomesubdir,fileroot); } if (Access_file_exists_p(filename) == false) { fprintf(stderr,"Unable to detect new version of genome index: genomebits128 file not available. This version of GSNAP is not backwards compatible.\n"); fprintf(stderr,"Looking specifically for %s\n",filename); FREE(filename); exit(9); return; } } else { fprintf(stderr,"Don't recognize genome type %d\n",genometype); abort(); } } else { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genome")+1,sizeof(char)); sprintf(filename,"%s/%s.genome",genomesubdir,fileroot); } Access_shmem_remove(filename); FREE(filename); return; } #endif T Genome_new (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T genometype, bool genome_lc_p, Access_mode_T access, bool sharedp) { T new = (T) MALLOC(sizeof(*new)); char *filename; bool compressedp = !genome_lc_p; char *comma; int npages; double seconds; new->compressedp = compressedp; if (compressedp == true) { if (genometype == GENOME_OLIGOS) { if (snps_root != NULL) { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char)); sprintf(filename,"%s/%s.genomecomp.%s",genomesubdir,fileroot,snps_root); } else { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomecomp")+1,sizeof(char)); sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot); } } else if (genometype == GENOME_BITS) { if (snps_root != NULL) { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char)); sprintf(filename,"%s/%s.genomebits128.%s",genomesubdir,fileroot,snps_root); } else { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genomebits128")+1,sizeof(char)); sprintf(filename,"%s/%s.genomebits128",genomesubdir,fileroot); } if (Access_file_exists_p(filename) == false) { fprintf(stderr,"Unable to detect new version of genome index: genomebits128 file not available. This version of GSNAP is not backwards compatible.\n"); fprintf(stderr,"Looking specifically for %s\n",filename); FREE(filename); FREE(new); exit(9); return (T) NULL; } } else { fprintf(stderr,"Don't recognize genome type %d\n",genometype); abort(); } } else { filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ strlen(".genome")+1,sizeof(char)); sprintf(filename,"%s/%s.genome",genomesubdir,fileroot); } if (compressedp == true) { new->chars = (char *) NULL; if (access == USE_ALLOCATE) { fprintf(stderr,"Allocating memory for compressed genome "); if (genometype == GENOME_OLIGOS) { fprintf(stderr,"(oligos)..."); } else if (genometype == GENOME_BITS) { fprintf(stderr,"(bits)..."); } if (sharedp == true) { new->blocks = (Genomecomp_T *) Access_allocate_shared(&new->access,&new->blocks_shmid,&new->blocks_key, &new->fd,&new->len,&seconds,filename,sizeof(Genomecomp_T)); } else { new->blocks = (Genomecomp_T *) Access_allocate_private(&new->access,&new->len,&seconds,filename,sizeof(Genomecomp_T)); } if (new->blocks == NULL) { fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B))\n"); exit(9); } else { comma = Genomicpos_commafmt(new->len); fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds); FREE(comma); } #ifdef HAVE_MMAP } else if (access == USE_MMAP_PRELOAD) { fprintf(stderr,"Pre-loading compressed genome "); if (genometype == GENOME_OLIGOS) { fprintf(stderr,"(oligos)..."); } else if (genometype == GENOME_BITS) { fprintf(stderr,"(bits)..."); } new->blocks = (Genomecomp_T *) Access_mmap_and_preload(&new->fd,&new->len,&npages,&seconds, filename,sizeof(Genomecomp_T)); if (new->blocks == NULL) { fprintf(stderr,"insufficient memory (will use disk file instead)\n"); new->access = FILEIO; } else { comma = Genomicpos_commafmt(new->len); fprintf(stderr,"done (%s bytes, %d pages, %.2f sec)\n",comma,npages,seconds); FREE(comma); new->access = MMAPPED; } } else if (access == USE_MMAP_ONLY) { new->blocks = (Genomecomp_T *) Access_mmap(&new->fd,&new->len,filename,/*randomp*/false); if (new->blocks == NULL) { fprintf(stderr,"Insufficient memory for genome mmap (will use disk file instead)\n"); new->access = FILEIO; } else { new->access = MMAPPED; } #endif } else if (access == USE_FILEIO) { new->blocks = (Genomecomp_T *) NULL; new->fd = Access_fileio(filename); new->access = FILEIO; } } else { new->blocks = (Genomecomp_T *) NULL; if (access == USE_ALLOCATE) { fprintf(stderr,"Allocating memory for uncompressed genome..."); if (sharedp == true) { new->chars = (char *) Access_allocate_shared(&new->access,&new->chars_shmid,&new->chars_key, &new->fd,&new->len,&seconds,filename,sizeof(char)); } else { new->chars = (char *) Access_allocate_private(&new->access,&new->len,&seconds,filename,sizeof(char)); } if (new->chars == NULL) { fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B))\n"); exit(9); } else { comma = Genomicpos_commafmt(new->len); fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds); FREE(comma); } #ifdef HAVE_MMAP } else if (access == USE_MMAP_PRELOAD) { fprintf(stderr,"Pre-loading uncompressed genome..."); new->chars = (char *) Access_mmap_and_preload(&new->fd,&new->len,&npages,&seconds, filename,sizeof(char)); if (new->chars == NULL) { fprintf(stderr,"insufficient memory (will use disk file instead)\n"); new->access = FILEIO; } else { comma = Genomicpos_commafmt(new->len); fprintf(stderr,"done (%s bytes, %d pages, %.2f sec)\n",comma,npages,seconds); FREE(comma); new->access = MMAPPED; } } else if (access == USE_MMAP_ONLY) { new->chars = (char *) Access_mmap(&new->fd,&new->len,filename,/*randomp*/false); if (new->chars == NULL) { fprintf(stderr,"Insufficient memory for genome mmap (will use disk file instead)\n"); new->access = FILEIO; } else { new->access = MMAPPED; } #endif } else if (access == USE_FILEIO) { new->chars = (char *) NULL; new->fd = Access_fileio(filename); new->access = FILEIO; } } #ifdef HAVE_PTHREAD if (new->access == FILEIO) { pthread_mutex_init(&new->read_mutex,NULL); } #endif FREE(filename); /* Initialize for Genome_next_char */ new->ptr = new->chars; new->left = 0U; if (new->compressedp == false) { if (new->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&new->read_mutex); #endif if (lseek(new->fd,/*left*/0U,SEEK_SET) < 0) { perror("Error in Genome_new"); exit(9); } #ifdef HAVE_PTHREAD pthread_mutex_unlock(&new->read_mutex); #endif } } return new; } static char complCode[128] = COMPLEMENT_LC; #if 0 static void make_complement_buffered (char *complement, char *sequence, Chrpos_T length) { int i, j; for (i = length-1, j = 0; i >= 0; i--, j++) { complement[j] = complCode[(int) sequence[i]]; } complement[length] = '\0'; return; } #endif static void make_complement_inplace (char *sequence, Chrpos_T length) { char temp; unsigned int i, j; for (i = 0, j = length-1; i < length/2; i++, j--) { temp = complCode[(int) sequence[i]]; sequence[i] = complCode[(int) sequence[j]]; sequence[j] = temp; } if (i == j) { sequence[i] = complCode[(int) sequence[i]]; } return; } /************************************************************************ * Read procedures ************************************************************************/ static void genomecomp_move_absolute (T this, off_t ptr) { off_t offset = ptr*((off_t) sizeof(Genomecomp_T)); if (lseek(this->fd,offset,SEEK_SET) < 0) { perror("Error in gmap, genomecomp_move_absolute"); exit(9); } return; } static Genomecomp_T genomecomp_read_current (T this) { Genomecomp_T value; char buffer[4]; read(this->fd,buffer,4); value = (buffer[3] & 0xff); value <<= 8; value |= (buffer[2] & 0xff); value <<= 8; value |= (buffer[1] & 0xff); value <<= 8; value |= (buffer[0] & 0xff); return value; } static char DEFAULT_CHARS[4] = {'A','C','G','T'}; static char DEFAULT_FLAGS[4] = {'N','N','N','N'}; static char X_FLAGS[4] = {'X','X','X','X'}; #ifdef EXTRACT_GENOMICSEG static char A_FLAGS[4] = {'A','A','A','A'}; #endif static char SNP_CHARS[4] = {' ',' ',' ',' '}; static char SNP_FLAGS[4] = {'A','C','G','T'}; static char *global_chars = DEFAULT_CHARS; static char *global_flags = DEFAULT_FLAGS; #if 0 void Genome_replace_x (void) { non_acgt[3] = 'N'; } #endif static const char *nucleotides[65536] = {"AAAAAAAA","CAAAAAAA","GAAAAAAA","TAAAAAAA","ACAAAAAA","CCAAAAAA","GCAAAAAA","TCAAAAAA", "AGAAAAAA","CGAAAAAA","GGAAAAAA","TGAAAAAA","ATAAAAAA","CTAAAAAA","GTAAAAAA","TTAAAAAA", "AACAAAAA","CACAAAAA","GACAAAAA","TACAAAAA","ACCAAAAA","CCCAAAAA","GCCAAAAA","TCCAAAAA", "AGCAAAAA","CGCAAAAA","GGCAAAAA","TGCAAAAA","ATCAAAAA","CTCAAAAA","GTCAAAAA","TTCAAAAA", "AAGAAAAA","CAGAAAAA","GAGAAAAA","TAGAAAAA","ACGAAAAA","CCGAAAAA","GCGAAAAA","TCGAAAAA", "AGGAAAAA","CGGAAAAA","GGGAAAAA","TGGAAAAA","ATGAAAAA","CTGAAAAA","GTGAAAAA","TTGAAAAA", "AATAAAAA","CATAAAAA","GATAAAAA","TATAAAAA","ACTAAAAA","CCTAAAAA","GCTAAAAA","TCTAAAAA", "AGTAAAAA","CGTAAAAA","GGTAAAAA","TGTAAAAA","ATTAAAAA","CTTAAAAA","GTTAAAAA","TTTAAAAA", "AAACAAAA","CAACAAAA","GAACAAAA","TAACAAAA","ACACAAAA","CCACAAAA","GCACAAAA","TCACAAAA", "AGACAAAA","CGACAAAA","GGACAAAA","TGACAAAA","ATACAAAA","CTACAAAA","GTACAAAA","TTACAAAA", "AACCAAAA","CACCAAAA","GACCAAAA","TACCAAAA","ACCCAAAA","CCCCAAAA","GCCCAAAA","TCCCAAAA", "AGCCAAAA","CGCCAAAA","GGCCAAAA","TGCCAAAA","ATCCAAAA","CTCCAAAA","GTCCAAAA","TTCCAAAA", "AAGCAAAA","CAGCAAAA","GAGCAAAA","TAGCAAAA","ACGCAAAA","CCGCAAAA","GCGCAAAA","TCGCAAAA", "AGGCAAAA","CGGCAAAA","GGGCAAAA","TGGCAAAA","ATGCAAAA","CTGCAAAA","GTGCAAAA","TTGCAAAA", "AATCAAAA","CATCAAAA","GATCAAAA","TATCAAAA","ACTCAAAA","CCTCAAAA","GCTCAAAA","TCTCAAAA", "AGTCAAAA","CGTCAAAA","GGTCAAAA","TGTCAAAA","ATTCAAAA","CTTCAAAA","GTTCAAAA","TTTCAAAA", "AAAGAAAA","CAAGAAAA","GAAGAAAA","TAAGAAAA","ACAGAAAA","CCAGAAAA","GCAGAAAA","TCAGAAAA", "AGAGAAAA","CGAGAAAA","GGAGAAAA","TGAGAAAA","ATAGAAAA","CTAGAAAA","GTAGAAAA","TTAGAAAA", "AACGAAAA","CACGAAAA","GACGAAAA","TACGAAAA","ACCGAAAA","CCCGAAAA","GCCGAAAA","TCCGAAAA", "AGCGAAAA","CGCGAAAA","GGCGAAAA","TGCGAAAA","ATCGAAAA","CTCGAAAA","GTCGAAAA","TTCGAAAA", "AAGGAAAA","CAGGAAAA","GAGGAAAA","TAGGAAAA","ACGGAAAA","CCGGAAAA","GCGGAAAA","TCGGAAAA", "AGGGAAAA","CGGGAAAA","GGGGAAAA","TGGGAAAA","ATGGAAAA","CTGGAAAA","GTGGAAAA","TTGGAAAA", "AATGAAAA","CATGAAAA","GATGAAAA","TATGAAAA","ACTGAAAA","CCTGAAAA","GCTGAAAA","TCTGAAAA", "AGTGAAAA","CGTGAAAA","GGTGAAAA","TGTGAAAA","ATTGAAAA","CTTGAAAA","GTTGAAAA","TTTGAAAA", "AAATAAAA","CAATAAAA","GAATAAAA","TAATAAAA","ACATAAAA","CCATAAAA","GCATAAAA","TCATAAAA", "AGATAAAA","CGATAAAA","GGATAAAA","TGATAAAA","ATATAAAA","CTATAAAA","GTATAAAA","TTATAAAA", "AACTAAAA","CACTAAAA","GACTAAAA","TACTAAAA","ACCTAAAA","CCCTAAAA","GCCTAAAA","TCCTAAAA", "AGCTAAAA","CGCTAAAA","GGCTAAAA","TGCTAAAA","ATCTAAAA","CTCTAAAA","GTCTAAAA","TTCTAAAA", "AAGTAAAA","CAGTAAAA","GAGTAAAA","TAGTAAAA","ACGTAAAA","CCGTAAAA","GCGTAAAA","TCGTAAAA", "AGGTAAAA","CGGTAAAA","GGGTAAAA","TGGTAAAA","ATGTAAAA","CTGTAAAA","GTGTAAAA","TTGTAAAA", "AATTAAAA","CATTAAAA","GATTAAAA","TATTAAAA","ACTTAAAA","CCTTAAAA","GCTTAAAA","TCTTAAAA", "AGTTAAAA","CGTTAAAA","GGTTAAAA","TGTTAAAA","ATTTAAAA","CTTTAAAA","GTTTAAAA","TTTTAAAA", "AAAACAAA","CAAACAAA","GAAACAAA","TAAACAAA","ACAACAAA","CCAACAAA","GCAACAAA","TCAACAAA", "AGAACAAA","CGAACAAA","GGAACAAA","TGAACAAA","ATAACAAA","CTAACAAA","GTAACAAA","TTAACAAA", "AACACAAA","CACACAAA","GACACAAA","TACACAAA","ACCACAAA","CCCACAAA","GCCACAAA","TCCACAAA", "AGCACAAA","CGCACAAA","GGCACAAA","TGCACAAA","ATCACAAA","CTCACAAA","GTCACAAA","TTCACAAA", "AAGACAAA","CAGACAAA","GAGACAAA","TAGACAAA","ACGACAAA","CCGACAAA","GCGACAAA","TCGACAAA", "AGGACAAA","CGGACAAA","GGGACAAA","TGGACAAA","ATGACAAA","CTGACAAA","GTGACAAA","TTGACAAA", "AATACAAA","CATACAAA","GATACAAA","TATACAAA","ACTACAAA","CCTACAAA","GCTACAAA","TCTACAAA", "AGTACAAA","CGTACAAA","GGTACAAA","TGTACAAA","ATTACAAA","CTTACAAA","GTTACAAA","TTTACAAA", "AAACCAAA","CAACCAAA","GAACCAAA","TAACCAAA","ACACCAAA","CCACCAAA","GCACCAAA","TCACCAAA", "AGACCAAA","CGACCAAA","GGACCAAA","TGACCAAA","ATACCAAA","CTACCAAA","GTACCAAA","TTACCAAA", "AACCCAAA","CACCCAAA","GACCCAAA","TACCCAAA","ACCCCAAA","CCCCCAAA","GCCCCAAA","TCCCCAAA", "AGCCCAAA","CGCCCAAA","GGCCCAAA","TGCCCAAA","ATCCCAAA","CTCCCAAA","GTCCCAAA","TTCCCAAA", "AAGCCAAA","CAGCCAAA","GAGCCAAA","TAGCCAAA","ACGCCAAA","CCGCCAAA","GCGCCAAA","TCGCCAAA", "AGGCCAAA","CGGCCAAA","GGGCCAAA","TGGCCAAA","ATGCCAAA","CTGCCAAA","GTGCCAAA","TTGCCAAA", "AATCCAAA","CATCCAAA","GATCCAAA","TATCCAAA","ACTCCAAA","CCTCCAAA","GCTCCAAA","TCTCCAAA", "AGTCCAAA","CGTCCAAA","GGTCCAAA","TGTCCAAA","ATTCCAAA","CTTCCAAA","GTTCCAAA","TTTCCAAA", "AAAGCAAA","CAAGCAAA","GAAGCAAA","TAAGCAAA","ACAGCAAA","CCAGCAAA","GCAGCAAA","TCAGCAAA", "AGAGCAAA","CGAGCAAA","GGAGCAAA","TGAGCAAA","ATAGCAAA","CTAGCAAA","GTAGCAAA","TTAGCAAA", "AACGCAAA","CACGCAAA","GACGCAAA","TACGCAAA","ACCGCAAA","CCCGCAAA","GCCGCAAA","TCCGCAAA", "AGCGCAAA","CGCGCAAA","GGCGCAAA","TGCGCAAA","ATCGCAAA","CTCGCAAA","GTCGCAAA","TTCGCAAA", "AAGGCAAA","CAGGCAAA","GAGGCAAA","TAGGCAAA","ACGGCAAA","CCGGCAAA","GCGGCAAA","TCGGCAAA", "AGGGCAAA","CGGGCAAA","GGGGCAAA","TGGGCAAA","ATGGCAAA","CTGGCAAA","GTGGCAAA","TTGGCAAA", "AATGCAAA","CATGCAAA","GATGCAAA","TATGCAAA","ACTGCAAA","CCTGCAAA","GCTGCAAA","TCTGCAAA", "AGTGCAAA","CGTGCAAA","GGTGCAAA","TGTGCAAA","ATTGCAAA","CTTGCAAA","GTTGCAAA","TTTGCAAA", "AAATCAAA","CAATCAAA","GAATCAAA","TAATCAAA","ACATCAAA","CCATCAAA","GCATCAAA","TCATCAAA", "AGATCAAA","CGATCAAA","GGATCAAA","TGATCAAA","ATATCAAA","CTATCAAA","GTATCAAA","TTATCAAA", "AACTCAAA","CACTCAAA","GACTCAAA","TACTCAAA","ACCTCAAA","CCCTCAAA","GCCTCAAA","TCCTCAAA", "AGCTCAAA","CGCTCAAA","GGCTCAAA","TGCTCAAA","ATCTCAAA","CTCTCAAA","GTCTCAAA","TTCTCAAA", "AAGTCAAA","CAGTCAAA","GAGTCAAA","TAGTCAAA","ACGTCAAA","CCGTCAAA","GCGTCAAA","TCGTCAAA", "AGGTCAAA","CGGTCAAA","GGGTCAAA","TGGTCAAA","ATGTCAAA","CTGTCAAA","GTGTCAAA","TTGTCAAA", "AATTCAAA","CATTCAAA","GATTCAAA","TATTCAAA","ACTTCAAA","CCTTCAAA","GCTTCAAA","TCTTCAAA", "AGTTCAAA","CGTTCAAA","GGTTCAAA","TGTTCAAA","ATTTCAAA","CTTTCAAA","GTTTCAAA","TTTTCAAA", "AAAAGAAA","CAAAGAAA","GAAAGAAA","TAAAGAAA","ACAAGAAA","CCAAGAAA","GCAAGAAA","TCAAGAAA", "AGAAGAAA","CGAAGAAA","GGAAGAAA","TGAAGAAA","ATAAGAAA","CTAAGAAA","GTAAGAAA","TTAAGAAA", "AACAGAAA","CACAGAAA","GACAGAAA","TACAGAAA","ACCAGAAA","CCCAGAAA","GCCAGAAA","TCCAGAAA", "AGCAGAAA","CGCAGAAA","GGCAGAAA","TGCAGAAA","ATCAGAAA","CTCAGAAA","GTCAGAAA","TTCAGAAA", "AAGAGAAA","CAGAGAAA","GAGAGAAA","TAGAGAAA","ACGAGAAA","CCGAGAAA","GCGAGAAA","TCGAGAAA", "AGGAGAAA","CGGAGAAA","GGGAGAAA","TGGAGAAA","ATGAGAAA","CTGAGAAA","GTGAGAAA","TTGAGAAA", "AATAGAAA","CATAGAAA","GATAGAAA","TATAGAAA","ACTAGAAA","CCTAGAAA","GCTAGAAA","TCTAGAAA", "AGTAGAAA","CGTAGAAA","GGTAGAAA","TGTAGAAA","ATTAGAAA","CTTAGAAA","GTTAGAAA","TTTAGAAA", "AAACGAAA","CAACGAAA","GAACGAAA","TAACGAAA","ACACGAAA","CCACGAAA","GCACGAAA","TCACGAAA", "AGACGAAA","CGACGAAA","GGACGAAA","TGACGAAA","ATACGAAA","CTACGAAA","GTACGAAA","TTACGAAA", "AACCGAAA","CACCGAAA","GACCGAAA","TACCGAAA","ACCCGAAA","CCCCGAAA","GCCCGAAA","TCCCGAAA", "AGCCGAAA","CGCCGAAA","GGCCGAAA","TGCCGAAA","ATCCGAAA","CTCCGAAA","GTCCGAAA","TTCCGAAA", "AAGCGAAA","CAGCGAAA","GAGCGAAA","TAGCGAAA","ACGCGAAA","CCGCGAAA","GCGCGAAA","TCGCGAAA", "AGGCGAAA","CGGCGAAA","GGGCGAAA","TGGCGAAA","ATGCGAAA","CTGCGAAA","GTGCGAAA","TTGCGAAA", "AATCGAAA","CATCGAAA","GATCGAAA","TATCGAAA","ACTCGAAA","CCTCGAAA","GCTCGAAA","TCTCGAAA", "AGTCGAAA","CGTCGAAA","GGTCGAAA","TGTCGAAA","ATTCGAAA","CTTCGAAA","GTTCGAAA","TTTCGAAA", "AAAGGAAA","CAAGGAAA","GAAGGAAA","TAAGGAAA","ACAGGAAA","CCAGGAAA","GCAGGAAA","TCAGGAAA", "AGAGGAAA","CGAGGAAA","GGAGGAAA","TGAGGAAA","ATAGGAAA","CTAGGAAA","GTAGGAAA","TTAGGAAA", "AACGGAAA","CACGGAAA","GACGGAAA","TACGGAAA","ACCGGAAA","CCCGGAAA","GCCGGAAA","TCCGGAAA", "AGCGGAAA","CGCGGAAA","GGCGGAAA","TGCGGAAA","ATCGGAAA","CTCGGAAA","GTCGGAAA","TTCGGAAA", 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"AGGATGTT","CGGATGTT","GGGATGTT","TGGATGTT","ATGATGTT","CTGATGTT","GTGATGTT","TTGATGTT", "AATATGTT","CATATGTT","GATATGTT","TATATGTT","ACTATGTT","CCTATGTT","GCTATGTT","TCTATGTT", "AGTATGTT","CGTATGTT","GGTATGTT","TGTATGTT","ATTATGTT","CTTATGTT","GTTATGTT","TTTATGTT", "AAACTGTT","CAACTGTT","GAACTGTT","TAACTGTT","ACACTGTT","CCACTGTT","GCACTGTT","TCACTGTT", "AGACTGTT","CGACTGTT","GGACTGTT","TGACTGTT","ATACTGTT","CTACTGTT","GTACTGTT","TTACTGTT", "AACCTGTT","CACCTGTT","GACCTGTT","TACCTGTT","ACCCTGTT","CCCCTGTT","GCCCTGTT","TCCCTGTT", "AGCCTGTT","CGCCTGTT","GGCCTGTT","TGCCTGTT","ATCCTGTT","CTCCTGTT","GTCCTGTT","TTCCTGTT", "AAGCTGTT","CAGCTGTT","GAGCTGTT","TAGCTGTT","ACGCTGTT","CCGCTGTT","GCGCTGTT","TCGCTGTT", "AGGCTGTT","CGGCTGTT","GGGCTGTT","TGGCTGTT","ATGCTGTT","CTGCTGTT","GTGCTGTT","TTGCTGTT", "AATCTGTT","CATCTGTT","GATCTGTT","TATCTGTT","ACTCTGTT","CCTCTGTT","GCTCTGTT","TCTCTGTT", "AGTCTGTT","CGTCTGTT","GGTCTGTT","TGTCTGTT","ATTCTGTT","CTTCTGTT","GTTCTGTT","TTTCTGTT", "AAAGTGTT","CAAGTGTT","GAAGTGTT","TAAGTGTT","ACAGTGTT","CCAGTGTT","GCAGTGTT","TCAGTGTT", "AGAGTGTT","CGAGTGTT","GGAGTGTT","TGAGTGTT","ATAGTGTT","CTAGTGTT","GTAGTGTT","TTAGTGTT", "AACGTGTT","CACGTGTT","GACGTGTT","TACGTGTT","ACCGTGTT","CCCGTGTT","GCCGTGTT","TCCGTGTT", "AGCGTGTT","CGCGTGTT","GGCGTGTT","TGCGTGTT","ATCGTGTT","CTCGTGTT","GTCGTGTT","TTCGTGTT", "AAGGTGTT","CAGGTGTT","GAGGTGTT","TAGGTGTT","ACGGTGTT","CCGGTGTT","GCGGTGTT","TCGGTGTT", "AGGGTGTT","CGGGTGTT","GGGGTGTT","TGGGTGTT","ATGGTGTT","CTGGTGTT","GTGGTGTT","TTGGTGTT", "AATGTGTT","CATGTGTT","GATGTGTT","TATGTGTT","ACTGTGTT","CCTGTGTT","GCTGTGTT","TCTGTGTT", "AGTGTGTT","CGTGTGTT","GGTGTGTT","TGTGTGTT","ATTGTGTT","CTTGTGTT","GTTGTGTT","TTTGTGTT", "AAATTGTT","CAATTGTT","GAATTGTT","TAATTGTT","ACATTGTT","CCATTGTT","GCATTGTT","TCATTGTT", "AGATTGTT","CGATTGTT","GGATTGTT","TGATTGTT","ATATTGTT","CTATTGTT","GTATTGTT","TTATTGTT", "AACTTGTT","CACTTGTT","GACTTGTT","TACTTGTT","ACCTTGTT","CCCTTGTT","GCCTTGTT","TCCTTGTT", "AGCTTGTT","CGCTTGTT","GGCTTGTT","TGCTTGTT","ATCTTGTT","CTCTTGTT","GTCTTGTT","TTCTTGTT", "AAGTTGTT","CAGTTGTT","GAGTTGTT","TAGTTGTT","ACGTTGTT","CCGTTGTT","GCGTTGTT","TCGTTGTT", "AGGTTGTT","CGGTTGTT","GGGTTGTT","TGGTTGTT","ATGTTGTT","CTGTTGTT","GTGTTGTT","TTGTTGTT", "AATTTGTT","CATTTGTT","GATTTGTT","TATTTGTT","ACTTTGTT","CCTTTGTT","GCTTTGTT","TCTTTGTT", "AGTTTGTT","CGTTTGTT","GGTTTGTT","TGTTTGTT","ATTTTGTT","CTTTTGTT","GTTTTGTT","TTTTTGTT", "AAAAATTT","CAAAATTT","GAAAATTT","TAAAATTT","ACAAATTT","CCAAATTT","GCAAATTT","TCAAATTT", "AGAAATTT","CGAAATTT","GGAAATTT","TGAAATTT","ATAAATTT","CTAAATTT","GTAAATTT","TTAAATTT", "AACAATTT","CACAATTT","GACAATTT","TACAATTT","ACCAATTT","CCCAATTT","GCCAATTT","TCCAATTT", "AGCAATTT","CGCAATTT","GGCAATTT","TGCAATTT","ATCAATTT","CTCAATTT","GTCAATTT","TTCAATTT", "AAGAATTT","CAGAATTT","GAGAATTT","TAGAATTT","ACGAATTT","CCGAATTT","GCGAATTT","TCGAATTT", "AGGAATTT","CGGAATTT","GGGAATTT","TGGAATTT","ATGAATTT","CTGAATTT","GTGAATTT","TTGAATTT", "AATAATTT","CATAATTT","GATAATTT","TATAATTT","ACTAATTT","CCTAATTT","GCTAATTT","TCTAATTT", "AGTAATTT","CGTAATTT","GGTAATTT","TGTAATTT","ATTAATTT","CTTAATTT","GTTAATTT","TTTAATTT", "AAACATTT","CAACATTT","GAACATTT","TAACATTT","ACACATTT","CCACATTT","GCACATTT","TCACATTT", "AGACATTT","CGACATTT","GGACATTT","TGACATTT","ATACATTT","CTACATTT","GTACATTT","TTACATTT", "AACCATTT","CACCATTT","GACCATTT","TACCATTT","ACCCATTT","CCCCATTT","GCCCATTT","TCCCATTT", "AGCCATTT","CGCCATTT","GGCCATTT","TGCCATTT","ATCCATTT","CTCCATTT","GTCCATTT","TTCCATTT", "AAGCATTT","CAGCATTT","GAGCATTT","TAGCATTT","ACGCATTT","CCGCATTT","GCGCATTT","TCGCATTT", "AGGCATTT","CGGCATTT","GGGCATTT","TGGCATTT","ATGCATTT","CTGCATTT","GTGCATTT","TTGCATTT", "AATCATTT","CATCATTT","GATCATTT","TATCATTT","ACTCATTT","CCTCATTT","GCTCATTT","TCTCATTT", "AGTCATTT","CGTCATTT","GGTCATTT","TGTCATTT","ATTCATTT","CTTCATTT","GTTCATTT","TTTCATTT", "AAAGATTT","CAAGATTT","GAAGATTT","TAAGATTT","ACAGATTT","CCAGATTT","GCAGATTT","TCAGATTT", "AGAGATTT","CGAGATTT","GGAGATTT","TGAGATTT","ATAGATTT","CTAGATTT","GTAGATTT","TTAGATTT", "AACGATTT","CACGATTT","GACGATTT","TACGATTT","ACCGATTT","CCCGATTT","GCCGATTT","TCCGATTT", "AGCGATTT","CGCGATTT","GGCGATTT","TGCGATTT","ATCGATTT","CTCGATTT","GTCGATTT","TTCGATTT", "AAGGATTT","CAGGATTT","GAGGATTT","TAGGATTT","ACGGATTT","CCGGATTT","GCGGATTT","TCGGATTT", "AGGGATTT","CGGGATTT","GGGGATTT","TGGGATTT","ATGGATTT","CTGGATTT","GTGGATTT","TTGGATTT", "AATGATTT","CATGATTT","GATGATTT","TATGATTT","ACTGATTT","CCTGATTT","GCTGATTT","TCTGATTT", "AGTGATTT","CGTGATTT","GGTGATTT","TGTGATTT","ATTGATTT","CTTGATTT","GTTGATTT","TTTGATTT", "AAATATTT","CAATATTT","GAATATTT","TAATATTT","ACATATTT","CCATATTT","GCATATTT","TCATATTT", "AGATATTT","CGATATTT","GGATATTT","TGATATTT","ATATATTT","CTATATTT","GTATATTT","TTATATTT", "AACTATTT","CACTATTT","GACTATTT","TACTATTT","ACCTATTT","CCCTATTT","GCCTATTT","TCCTATTT", "AGCTATTT","CGCTATTT","GGCTATTT","TGCTATTT","ATCTATTT","CTCTATTT","GTCTATTT","TTCTATTT", "AAGTATTT","CAGTATTT","GAGTATTT","TAGTATTT","ACGTATTT","CCGTATTT","GCGTATTT","TCGTATTT", "AGGTATTT","CGGTATTT","GGGTATTT","TGGTATTT","ATGTATTT","CTGTATTT","GTGTATTT","TTGTATTT", "AATTATTT","CATTATTT","GATTATTT","TATTATTT","ACTTATTT","CCTTATTT","GCTTATTT","TCTTATTT", "AGTTATTT","CGTTATTT","GGTTATTT","TGTTATTT","ATTTATTT","CTTTATTT","GTTTATTT","TTTTATTT", "AAAACTTT","CAAACTTT","GAAACTTT","TAAACTTT","ACAACTTT","CCAACTTT","GCAACTTT","TCAACTTT", "AGAACTTT","CGAACTTT","GGAACTTT","TGAACTTT","ATAACTTT","CTAACTTT","GTAACTTT","TTAACTTT", "AACACTTT","CACACTTT","GACACTTT","TACACTTT","ACCACTTT","CCCACTTT","GCCACTTT","TCCACTTT", "AGCACTTT","CGCACTTT","GGCACTTT","TGCACTTT","ATCACTTT","CTCACTTT","GTCACTTT","TTCACTTT", "AAGACTTT","CAGACTTT","GAGACTTT","TAGACTTT","ACGACTTT","CCGACTTT","GCGACTTT","TCGACTTT", "AGGACTTT","CGGACTTT","GGGACTTT","TGGACTTT","ATGACTTT","CTGACTTT","GTGACTTT","TTGACTTT", "AATACTTT","CATACTTT","GATACTTT","TATACTTT","ACTACTTT","CCTACTTT","GCTACTTT","TCTACTTT", "AGTACTTT","CGTACTTT","GGTACTTT","TGTACTTT","ATTACTTT","CTTACTTT","GTTACTTT","TTTACTTT", "AAACCTTT","CAACCTTT","GAACCTTT","TAACCTTT","ACACCTTT","CCACCTTT","GCACCTTT","TCACCTTT", "AGACCTTT","CGACCTTT","GGACCTTT","TGACCTTT","ATACCTTT","CTACCTTT","GTACCTTT","TTACCTTT", "AACCCTTT","CACCCTTT","GACCCTTT","TACCCTTT","ACCCCTTT","CCCCCTTT","GCCCCTTT","TCCCCTTT", "AGCCCTTT","CGCCCTTT","GGCCCTTT","TGCCCTTT","ATCCCTTT","CTCCCTTT","GTCCCTTT","TTCCCTTT", "AAGCCTTT","CAGCCTTT","GAGCCTTT","TAGCCTTT","ACGCCTTT","CCGCCTTT","GCGCCTTT","TCGCCTTT", "AGGCCTTT","CGGCCTTT","GGGCCTTT","TGGCCTTT","ATGCCTTT","CTGCCTTT","GTGCCTTT","TTGCCTTT", "AATCCTTT","CATCCTTT","GATCCTTT","TATCCTTT","ACTCCTTT","CCTCCTTT","GCTCCTTT","TCTCCTTT", "AGTCCTTT","CGTCCTTT","GGTCCTTT","TGTCCTTT","ATTCCTTT","CTTCCTTT","GTTCCTTT","TTTCCTTT", "AAAGCTTT","CAAGCTTT","GAAGCTTT","TAAGCTTT","ACAGCTTT","CCAGCTTT","GCAGCTTT","TCAGCTTT", "AGAGCTTT","CGAGCTTT","GGAGCTTT","TGAGCTTT","ATAGCTTT","CTAGCTTT","GTAGCTTT","TTAGCTTT", "AACGCTTT","CACGCTTT","GACGCTTT","TACGCTTT","ACCGCTTT","CCCGCTTT","GCCGCTTT","TCCGCTTT", "AGCGCTTT","CGCGCTTT","GGCGCTTT","TGCGCTTT","ATCGCTTT","CTCGCTTT","GTCGCTTT","TTCGCTTT", "AAGGCTTT","CAGGCTTT","GAGGCTTT","TAGGCTTT","ACGGCTTT","CCGGCTTT","GCGGCTTT","TCGGCTTT", "AGGGCTTT","CGGGCTTT","GGGGCTTT","TGGGCTTT","ATGGCTTT","CTGGCTTT","GTGGCTTT","TTGGCTTT", "AATGCTTT","CATGCTTT","GATGCTTT","TATGCTTT","ACTGCTTT","CCTGCTTT","GCTGCTTT","TCTGCTTT", "AGTGCTTT","CGTGCTTT","GGTGCTTT","TGTGCTTT","ATTGCTTT","CTTGCTTT","GTTGCTTT","TTTGCTTT", "AAATCTTT","CAATCTTT","GAATCTTT","TAATCTTT","ACATCTTT","CCATCTTT","GCATCTTT","TCATCTTT", "AGATCTTT","CGATCTTT","GGATCTTT","TGATCTTT","ATATCTTT","CTATCTTT","GTATCTTT","TTATCTTT", "AACTCTTT","CACTCTTT","GACTCTTT","TACTCTTT","ACCTCTTT","CCCTCTTT","GCCTCTTT","TCCTCTTT", "AGCTCTTT","CGCTCTTT","GGCTCTTT","TGCTCTTT","ATCTCTTT","CTCTCTTT","GTCTCTTT","TTCTCTTT", "AAGTCTTT","CAGTCTTT","GAGTCTTT","TAGTCTTT","ACGTCTTT","CCGTCTTT","GCGTCTTT","TCGTCTTT", "AGGTCTTT","CGGTCTTT","GGGTCTTT","TGGTCTTT","ATGTCTTT","CTGTCTTT","GTGTCTTT","TTGTCTTT", "AATTCTTT","CATTCTTT","GATTCTTT","TATTCTTT","ACTTCTTT","CCTTCTTT","GCTTCTTT","TCTTCTTT", "AGTTCTTT","CGTTCTTT","GGTTCTTT","TGTTCTTT","ATTTCTTT","CTTTCTTT","GTTTCTTT","TTTTCTTT", "AAAAGTTT","CAAAGTTT","GAAAGTTT","TAAAGTTT","ACAAGTTT","CCAAGTTT","GCAAGTTT","TCAAGTTT", "AGAAGTTT","CGAAGTTT","GGAAGTTT","TGAAGTTT","ATAAGTTT","CTAAGTTT","GTAAGTTT","TTAAGTTT", "AACAGTTT","CACAGTTT","GACAGTTT","TACAGTTT","ACCAGTTT","CCCAGTTT","GCCAGTTT","TCCAGTTT", "AGCAGTTT","CGCAGTTT","GGCAGTTT","TGCAGTTT","ATCAGTTT","CTCAGTTT","GTCAGTTT","TTCAGTTT", "AAGAGTTT","CAGAGTTT","GAGAGTTT","TAGAGTTT","ACGAGTTT","CCGAGTTT","GCGAGTTT","TCGAGTTT", "AGGAGTTT","CGGAGTTT","GGGAGTTT","TGGAGTTT","ATGAGTTT","CTGAGTTT","GTGAGTTT","TTGAGTTT", "AATAGTTT","CATAGTTT","GATAGTTT","TATAGTTT","ACTAGTTT","CCTAGTTT","GCTAGTTT","TCTAGTTT", "AGTAGTTT","CGTAGTTT","GGTAGTTT","TGTAGTTT","ATTAGTTT","CTTAGTTT","GTTAGTTT","TTTAGTTT", "AAACGTTT","CAACGTTT","GAACGTTT","TAACGTTT","ACACGTTT","CCACGTTT","GCACGTTT","TCACGTTT", "AGACGTTT","CGACGTTT","GGACGTTT","TGACGTTT","ATACGTTT","CTACGTTT","GTACGTTT","TTACGTTT", "AACCGTTT","CACCGTTT","GACCGTTT","TACCGTTT","ACCCGTTT","CCCCGTTT","GCCCGTTT","TCCCGTTT", "AGCCGTTT","CGCCGTTT","GGCCGTTT","TGCCGTTT","ATCCGTTT","CTCCGTTT","GTCCGTTT","TTCCGTTT", "AAGCGTTT","CAGCGTTT","GAGCGTTT","TAGCGTTT","ACGCGTTT","CCGCGTTT","GCGCGTTT","TCGCGTTT", "AGGCGTTT","CGGCGTTT","GGGCGTTT","TGGCGTTT","ATGCGTTT","CTGCGTTT","GTGCGTTT","TTGCGTTT", "AATCGTTT","CATCGTTT","GATCGTTT","TATCGTTT","ACTCGTTT","CCTCGTTT","GCTCGTTT","TCTCGTTT", "AGTCGTTT","CGTCGTTT","GGTCGTTT","TGTCGTTT","ATTCGTTT","CTTCGTTT","GTTCGTTT","TTTCGTTT", "AAAGGTTT","CAAGGTTT","GAAGGTTT","TAAGGTTT","ACAGGTTT","CCAGGTTT","GCAGGTTT","TCAGGTTT", "AGAGGTTT","CGAGGTTT","GGAGGTTT","TGAGGTTT","ATAGGTTT","CTAGGTTT","GTAGGTTT","TTAGGTTT", "AACGGTTT","CACGGTTT","GACGGTTT","TACGGTTT","ACCGGTTT","CCCGGTTT","GCCGGTTT","TCCGGTTT", "AGCGGTTT","CGCGGTTT","GGCGGTTT","TGCGGTTT","ATCGGTTT","CTCGGTTT","GTCGGTTT","TTCGGTTT", "AAGGGTTT","CAGGGTTT","GAGGGTTT","TAGGGTTT","ACGGGTTT","CCGGGTTT","GCGGGTTT","TCGGGTTT", "AGGGGTTT","CGGGGTTT","GGGGGTTT","TGGGGTTT","ATGGGTTT","CTGGGTTT","GTGGGTTT","TTGGGTTT", "AATGGTTT","CATGGTTT","GATGGTTT","TATGGTTT","ACTGGTTT","CCTGGTTT","GCTGGTTT","TCTGGTTT", "AGTGGTTT","CGTGGTTT","GGTGGTTT","TGTGGTTT","ATTGGTTT","CTTGGTTT","GTTGGTTT","TTTGGTTT", "AAATGTTT","CAATGTTT","GAATGTTT","TAATGTTT","ACATGTTT","CCATGTTT","GCATGTTT","TCATGTTT", "AGATGTTT","CGATGTTT","GGATGTTT","TGATGTTT","ATATGTTT","CTATGTTT","GTATGTTT","TTATGTTT", "AACTGTTT","CACTGTTT","GACTGTTT","TACTGTTT","ACCTGTTT","CCCTGTTT","GCCTGTTT","TCCTGTTT", "AGCTGTTT","CGCTGTTT","GGCTGTTT","TGCTGTTT","ATCTGTTT","CTCTGTTT","GTCTGTTT","TTCTGTTT", "AAGTGTTT","CAGTGTTT","GAGTGTTT","TAGTGTTT","ACGTGTTT","CCGTGTTT","GCGTGTTT","TCGTGTTT", "AGGTGTTT","CGGTGTTT","GGGTGTTT","TGGTGTTT","ATGTGTTT","CTGTGTTT","GTGTGTTT","TTGTGTTT", "AATTGTTT","CATTGTTT","GATTGTTT","TATTGTTT","ACTTGTTT","CCTTGTTT","GCTTGTTT","TCTTGTTT", "AGTTGTTT","CGTTGTTT","GGTTGTTT","TGTTGTTT","ATTTGTTT","CTTTGTTT","GTTTGTTT","TTTTGTTT", "AAAATTTT","CAAATTTT","GAAATTTT","TAAATTTT","ACAATTTT","CCAATTTT","GCAATTTT","TCAATTTT", "AGAATTTT","CGAATTTT","GGAATTTT","TGAATTTT","ATAATTTT","CTAATTTT","GTAATTTT","TTAATTTT", "AACATTTT","CACATTTT","GACATTTT","TACATTTT","ACCATTTT","CCCATTTT","GCCATTTT","TCCATTTT", "AGCATTTT","CGCATTTT","GGCATTTT","TGCATTTT","ATCATTTT","CTCATTTT","GTCATTTT","TTCATTTT", "AAGATTTT","CAGATTTT","GAGATTTT","TAGATTTT","ACGATTTT","CCGATTTT","GCGATTTT","TCGATTTT", "AGGATTTT","CGGATTTT","GGGATTTT","TGGATTTT","ATGATTTT","CTGATTTT","GTGATTTT","TTGATTTT", "AATATTTT","CATATTTT","GATATTTT","TATATTTT","ACTATTTT","CCTATTTT","GCTATTTT","TCTATTTT", "AGTATTTT","CGTATTTT","GGTATTTT","TGTATTTT","ATTATTTT","CTTATTTT","GTTATTTT","TTTATTTT", "AAACTTTT","CAACTTTT","GAACTTTT","TAACTTTT","ACACTTTT","CCACTTTT","GCACTTTT","TCACTTTT", "AGACTTTT","CGACTTTT","GGACTTTT","TGACTTTT","ATACTTTT","CTACTTTT","GTACTTTT","TTACTTTT", "AACCTTTT","CACCTTTT","GACCTTTT","TACCTTTT","ACCCTTTT","CCCCTTTT","GCCCTTTT","TCCCTTTT", "AGCCTTTT","CGCCTTTT","GGCCTTTT","TGCCTTTT","ATCCTTTT","CTCCTTTT","GTCCTTTT","TTCCTTTT", "AAGCTTTT","CAGCTTTT","GAGCTTTT","TAGCTTTT","ACGCTTTT","CCGCTTTT","GCGCTTTT","TCGCTTTT", "AGGCTTTT","CGGCTTTT","GGGCTTTT","TGGCTTTT","ATGCTTTT","CTGCTTTT","GTGCTTTT","TTGCTTTT", "AATCTTTT","CATCTTTT","GATCTTTT","TATCTTTT","ACTCTTTT","CCTCTTTT","GCTCTTTT","TCTCTTTT", "AGTCTTTT","CGTCTTTT","GGTCTTTT","TGTCTTTT","ATTCTTTT","CTTCTTTT","GTTCTTTT","TTTCTTTT", "AAAGTTTT","CAAGTTTT","GAAGTTTT","TAAGTTTT","ACAGTTTT","CCAGTTTT","GCAGTTTT","TCAGTTTT", "AGAGTTTT","CGAGTTTT","GGAGTTTT","TGAGTTTT","ATAGTTTT","CTAGTTTT","GTAGTTTT","TTAGTTTT", "AACGTTTT","CACGTTTT","GACGTTTT","TACGTTTT","ACCGTTTT","CCCGTTTT","GCCGTTTT","TCCGTTTT", "AGCGTTTT","CGCGTTTT","GGCGTTTT","TGCGTTTT","ATCGTTTT","CTCGTTTT","GTCGTTTT","TTCGTTTT", "AAGGTTTT","CAGGTTTT","GAGGTTTT","TAGGTTTT","ACGGTTTT","CCGGTTTT","GCGGTTTT","TCGGTTTT", "AGGGTTTT","CGGGTTTT","GGGGTTTT","TGGGTTTT","ATGGTTTT","CTGGTTTT","GTGGTTTT","TTGGTTTT", "AATGTTTT","CATGTTTT","GATGTTTT","TATGTTTT","ACTGTTTT","CCTGTTTT","GCTGTTTT","TCTGTTTT", "AGTGTTTT","CGTGTTTT","GGTGTTTT","TGTGTTTT","ATTGTTTT","CTTGTTTT","GTTGTTTT","TTTGTTTT", "AAATTTTT","CAATTTTT","GAATTTTT","TAATTTTT","ACATTTTT","CCATTTTT","GCATTTTT","TCATTTTT", "AGATTTTT","CGATTTTT","GGATTTTT","TGATTTTT","ATATTTTT","CTATTTTT","GTATTTTT","TTATTTTT", "AACTTTTT","CACTTTTT","GACTTTTT","TACTTTTT","ACCTTTTT","CCCTTTTT","GCCTTTTT","TCCTTTTT", "AGCTTTTT","CGCTTTTT","GGCTTTTT","TGCTTTTT","ATCTTTTT","CTCTTTTT","GTCTTTTT","TTCTTTTT", "AAGTTTTT","CAGTTTTT","GAGTTTTT","TAGTTTTT","ACGTTTTT","CCGTTTTT","GCGTTTTT","TCGTTTTT", "AGGTTTTT","CGGTTTTT","GGGTTTTT","TGGTTTTT","ATGTTTTT","CTGTTTTT","GTGTTTTT","TTGTTTTT", "AATTTTTT","CATTTTTT","GATTTTTT","TATTTTTT","ACTTTTTT","CCTTTTTT","GCTTTTTT","TCTTTTTT", "AGTTTTTT","CGTTTTTT","GGTTTTTT","TGTTTTTT","ATTTTTTT","CTTTTTTT","GTTTTTTT","TTTTTTTT"}; static void uncompress_fileio (char *gbuffer1, T this, Univcoord_T startpos, Univcoord_T endpos, const char defaultchars[], const char flagchars[]) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; char Buffer[32]; int startdiscard, enddiscard, i; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ genomecomp_move_absolute(this,ptr); high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < enddiscard; i++) { *gbuffer1++ = Buffer[i]; } } else { genomecomp_move_absolute(this,ptr); high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < 32; i++) { *gbuffer1++ = Buffer[i]; } ptr += 3; while (ptr < endblock) { high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { *gbuffer1++ = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { *gbuffer1++ = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } ptr += 3; } if (enddiscard > 0) { high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = 0; i < enddiscard; i++) { *gbuffer1++ = Buffer[i]; } } } return; } static void ntcounts_fileio (Univcoord_T *na, Univcoord_T *nc, Univcoord_T *ng, Univcoord_T *nt, T this, Univcoord_T startpos, Univcoord_T endpos, const char defaultchars[], const char flagchars[]) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; char Buffer[32], c; int startdiscard, enddiscard, i; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ genomecomp_move_absolute(this,ptr); high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < enddiscard; i++) { switch (Buffer[i]) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } } } else { genomecomp_move_absolute(this,ptr); high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < 32; i++) { switch (Buffer[i]) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } } ptr += 3; while (ptr < endblock) { high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { c = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); switch (c) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { c = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); switch (c) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } high >>= 2; flags >>= 1; } ptr += 3; } if (enddiscard > 0) { high = genomecomp_read_current(this); low = genomecomp_read_current(this); flags = genomecomp_read_current(this); for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = 0; i < enddiscard; i++) { switch (Buffer[i]) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } } } } return; } static void uncompress_mmap_bitbybit (char *gbuffer1, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos, const char defaultchars[], const char flagchars[]) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; char Buffer[32]; int startdiscard, enddiscard, i; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < enddiscard; i++) { *gbuffer1++ = Buffer[i]; } } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < 32; i++) { *gbuffer1++ = Buffer[i]; } ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { *gbuffer1++ = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { *gbuffer1++ = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = 0; i < enddiscard; i++) { *gbuffer1++ = Buffer[i]; } } } return; } void Genome_uncompress_mmap (char *gbuffer1, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; char Buffer[32]; int startdiscard, enddiscard; Univcoord_T k = 0, i; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[low >> 16],8); memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[high >> 16],8); if (flags) { for (i = 0; i < 32; i++) { if (flags & 1U) { Buffer[i] = 'N'; } flags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard)); } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[low >> 16],8); memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[high >> 16],8); if (flags) { for (i = 0; i < 32; i++) { if (flags & 1U) { Buffer[i] = 'N'; } flags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard); ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(&(gbuffer1[k]),nucleotides[low & 0x0000FFFF],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[low >> 16],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[high & 0x0000FFFF],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[high >> 16],8); k += 8; if (flags) { for (i = k - 32; i < k; i++) { if (flags & 1U) { gbuffer1[i] = 'N'; } flags >>= 1; } } ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[low >> 16],8); memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[high >> 16],8); if (flags) { for (i = 0; i < 32; i++) { if (flags & 1U) { Buffer[i] = 'N'; } flags >>= 1; } } memcpy(&(gbuffer1[k]),Buffer,enddiscard); } } return; } /* Same as Genome_uncompress_mmap, except does not perform bigendian conversion */ void Genome_uncompress_memory (char *gbuffer1, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; char Buffer[32]; int startdiscard, enddiscard; Univcoord_T k = 0, i; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #if 0 high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[low >> 16],8); memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[high >> 16],8); if (flags) { for (i = 0; i < 32; i++) { if (flags & 1U) { Buffer[i] = 'N'; } flags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard)); } else { #if 0 high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[low >> 16],8); memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[high >> 16],8); if (flags) { for (i = 0; i < 32; i++) { if (flags & 1U) { Buffer[i] = 'N'; } flags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard); ptr += 3; while (ptr < endblock) { #if 0 high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(&(gbuffer1[k]),nucleotides[low & 0x0000FFFF],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[low >> 16],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[high & 0x0000FFFF],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[high >> 16],8); k += 8; if (flags) { for (i = k - 32; i < k; i++) { if (flags & 1U) { gbuffer1[i] = 'N'; } flags >>= 1; } } ptr += 3; } if (enddiscard > 0) { #if 0 high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[low >> 16],8); memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[high >> 16],8); if (flags) { for (i = 0; i < 32; i++) { if (flags & 1U) { Buffer[i] = 'N'; } flags >>= 1; } } memcpy(&(gbuffer1[k]),Buffer,enddiscard); } } return; } /* Correct procedure should look at alt high/low and normal flags, and substitute N based on normal flags */ /* May not handle wildcard positions correctly. A wildcard occurs if ref == alt && ref_flag == 0 && alt_flag == 1 */ static void uncompress_mmap_snps_subst (char *gbuffer1, Genomecomp_T *refblocks, Genomecomp_T *altblocks, Univcoord_T startpos, Univcoord_T endpos) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T althigh, altlow, refflags; char Buffer[32]; int startdiscard, enddiscard, i, k, k1; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN althigh = Bigendian_convert_uint(altblocks[ptr]); altlow = Bigendian_convert_uint(altblocks[ptr+1]); refflags = Bigendian_convert_uint(refblocks[ptr+2]); #else althigh = altblocks[ptr]; altlow = altblocks[ptr+1]; refflags = refblocks[ptr+2]; #endif memcpy(Buffer,nucleotides[altlow & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[altlow >> 16],8); memcpy(&(Buffer[16]),nucleotides[althigh & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[althigh >> 16],8); if (refflags) { for (i = 0; i < 16; i++) { if (refflags & 1U) { Buffer[i] = 'N'; } altlow >>= 2; refflags >>= 1; } for ( ; i < 32; i++) { if (refflags & 1U) { Buffer[i] = 'N'; } althigh >>= 2; refflags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard)); } else { #ifdef WORDS_BIGENDIAN althigh = Bigendian_convert_uint(altblocks[ptr]); altlow = Bigendian_convert_uint(altblocks[ptr+1]); refflags = Bigendian_convert_uint(refblocks[ptr+2]); #else althigh = altblocks[ptr]; altlow = altblocks[ptr+1]; refflags = refblocks[ptr+2]; #endif memcpy(Buffer,nucleotides[altlow & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[altlow >> 16],8); memcpy(&(Buffer[16]),nucleotides[althigh & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[althigh >> 16],8); if (refflags) { for (i = 0; i < 16; i++) { if (refflags & 1U) { Buffer[i] = 'N'; } altlow >>= 2; refflags >>= 1; } for ( ; i < 32; i++) { if (refflags & 1U) { Buffer[i] = 'N'; } althigh >>= 2; refflags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard); ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN althigh = Bigendian_convert_uint(altblocks[ptr]); altlow = Bigendian_convert_uint(altblocks[ptr+1]); refflags = Bigendian_convert_uint(refblocks[ptr+2]); #else althigh = altblocks[ptr]; altlow = altblocks[ptr+1]; refflags = refblocks[ptr+2]; #endif memcpy(&(gbuffer1[k]),nucleotides[altlow & 0x0000FFFF],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[altlow >> 16],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[althigh & 0x0000FFFF],8); k += 8; memcpy(&(gbuffer1[k]),nucleotides[althigh >> 16],8); k += 8; if (refflags) { k1 = k - 32; for (i = 0; i < 16; i++, k1++) { if (refflags & 1U) { gbuffer1[k1] = 'N'; } altlow >>= 2; refflags >>= 1; } for ( ; i < 32; i++, k1++) { if (refflags & 1U) { gbuffer1[k1] = 'N'; } althigh >>= 2; refflags >>= 1; } } ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN althigh = Bigendian_convert_uint(altblocks[ptr]); altlow = Bigendian_convert_uint(altblocks[ptr+1]); refflags = Bigendian_convert_uint(refblocks[ptr+2]); #else althigh = altblocks[ptr]; altlow = altblocks[ptr+1]; refflags = refblocks[ptr+2]; #endif memcpy(Buffer,nucleotides[altlow & 0x0000FFFF],8); memcpy(&(Buffer[8]),nucleotides[altlow >> 16],8); memcpy(&(Buffer[16]),nucleotides[althigh & 0x0000FFFF],8); memcpy(&(Buffer[24]),nucleotides[althigh >> 16],8); if (refflags) { for (i = 0; i < 16; i++) { if (refflags & 1U) { Buffer[i] = 'N'; } altlow >>= 2; refflags >>= 1; } for ( ; i < 32; i++) { if (refflags & 1U) { Buffer[i] = 'N'; } althigh >>= 2; refflags >>= 1; } } memcpy(&(gbuffer1[k]),Buffer,enddiscard); } } return; } #if 0 /*01234567890123456789012345678901*/ static char EMPTY_32[32] = " "; static void uncompress_mmap_snps_only (char *gbuffer1, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos, const char flagchars[]) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; char Buffer[32]; int startdiscard, enddiscard, i; Univcoord_T k = 0; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,EMPTY_32,32); if (flags) { for (i = 0; i < 16; i++) { if (flags & 1U) { Buffer[i] = flagchars[low & 3U]; } low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { if (flags & 1U) { Buffer[i] = flagchars[high & 3U]; } high >>= 2; flags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard)); } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,EMPTY_32,32); if (flags) { for (i = 0; i < 16; i++) { if (flags & 1U) { Buffer[i] = flagchars[low & 3U]; } low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { if (flags & 1U) { Buffer[i] = flagchars[high & 3U]; } high >>= 2; flags >>= 1; } } memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard); ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(&(gbuffer1[k]),EMPTY_32,32); if (!flags) { k += 32; } else { for (i = 0; i < 16; i++, k++) { if (flags & 1U) { gbuffer1[k] = flagchars[low & 3U]; } low >>= 2; flags >>= 1; } for ( ; i < 32; i++, k++) { if (flags & 1U) { gbuffer1[k] = flagchars[high & 3U]; } high >>= 2; flags >>= 1; } } ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif memcpy(Buffer,EMPTY_32,32); if (flags) { for (i = 0; i < 16; i++) { if (flags & 1U) { Buffer[i] = flagchars[low & 3U]; } low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { if (flags & 1U) { Buffer[i] = flagchars[high & 3U]; } high >>= 2; flags >>= 1; } } memcpy(&(gbuffer1[k]),Buffer,enddiscard); } } return; } #endif #define LOW_TWO_BITS 0x3; static char uncompress_one_char (Genomecomp_T *blocks, Univcoord_T pos, char flagchar, char chartable[]) { Univcoord_T ptr; Genomecomp_T high, low, flags; int bit, c; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = pos/32U*3; bit = pos % 32; #ifdef WORDS_BIGENDIAN flags = Bigendian_convert_uint(blocks[ptr+2]); #else flags = blocks[ptr+2]; #endif if (flags & (1 << bit)) { return flagchar; } else if (bit < 16) { #ifdef WORDS_BIGENDIAN low = Bigendian_convert_uint(blocks[ptr+1]); #else low = blocks[ptr+1]; #endif c = (low >> (bit+bit)) & LOW_TWO_BITS; return chartable[c]; } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); #else high = blocks[ptr]; #endif c = (high >> (bit+bit-32)) & LOW_TWO_BITS; return chartable[c]; } } static char CHARTABLE[4] = {'A','C','G','T'}; static char uncompress_one_char_ignore_flags (Genomecomp_T *blocks, Univcoord_T pos) { Univcoord_T ptr; Genomecomp_T high, low; int bit, c; /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = pos/32U*3; bit = pos % 32; if (bit < 16) { #ifdef WORDS_BIGENDIAN low = Bigendian_convert_uint(blocks[ptr+1]); #else low = blocks[ptr+1]; #endif c = (low >> (bit+bit)) & LOW_TWO_BITS; return CHARTABLE[c]; } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); #else high = blocks[ptr]; #endif c = (high >> (bit+bit-32)) & LOW_TWO_BITS; return CHARTABLE[c]; } } static void Genome_ntcounts_mmap (Univcoord_T *na, Univcoord_T *nc, Univcoord_T *ng, Univcoord_T *nt, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos, const char defaultchars[], const char flagchars[]) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; char Buffer[32], c; int startdiscard, enddiscard, i; /* *na = *nc = *ng = *nt = 0; */ /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < enddiscard; i++) { switch (Buffer[i]) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } } } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = startdiscard; i < 32; i++) { switch (Buffer[i]) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } } ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { c = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); switch (c) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { c = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); switch (c) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } high >>= 2; flags >>= 1; } ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[low & 3U] : defaultchars[low & 3U]); low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { Buffer[i] = (char) ((flags & 1U) ? flagchars[high & 3U] : defaultchars[high & 3U]); high >>= 2; flags >>= 1; } for (i = 0; i < enddiscard; i++) { switch (Buffer[i]) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } } } } return; } #ifdef DEBUG3 static bool check_nucleotide (unsigned char nucleotide, char sequence) { printf("%d %c\n",nucleotide,sequence); switch (sequence) { case 'A': if (nucleotide != 0) return true; break; case 'C': if (nucleotide != 1) return true; break; case 'G': if (nucleotide != 2) return true; break; case 'T': if (nucleotide != 3) return true; break; } return false; } #endif #if 0 static bool uncompress_mmap_nucleotides_wstatus (unsigned char *gbuffer, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, startdiscard, enddiscard, ptr; Genomecomp_T high, low, flags; int i; #ifdef DEBUG3 char gbuffer_debug[1024]; #endif /* sequence = (char *) CALLOC(length+1,sizeof(char)); */ #ifdef DEBUG3 Genome_uncompress_mmap(gbuffer_debug,blocks,startpos,endpos); #endif ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif flags >>= startdiscard; if (startdiscard < 16) { low >>= (startdiscard+startdiscard); while (startdiscard < enddiscard && startdiscard < 16) { if (flags & 0x01) { /* return false; */ } *gbuffer++ = (unsigned char) (low & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 1, startdiscard %d, enddiscard %d\n",startdiscard,enddiscard); abort(); } #endif flags >>= 1; low >>= 2; startdiscard++; } } if (enddiscard >= 16) { startdiscard -= 16; enddiscard -= 16; high >>= (startdiscard+startdiscard); while (startdiscard < enddiscard) { if (flags & 0x01) { /* return false; */ } *gbuffer++ = (unsigned char) (high & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 2\n"); abort(); } #endif flags >>= 1; high >>= 2; startdiscard++; } } return true; } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif flags >>= startdiscard; if (startdiscard < 16) { low >>= (startdiscard+startdiscard); while (startdiscard < 16) { if (flags & 0x01) { /* return false; */ } *gbuffer++ = (unsigned char) (low & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 3\n"); abort(); } #endif flags >>= 1; low >>= 2; startdiscard++; } } startdiscard -= 16; high >>= (startdiscard+startdiscard); while (startdiscard < 16) { if (flags & 0x01) { /* return false; */ } *gbuffer++ = (unsigned char) (high & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 4, startdiscard %d (after subtracting 16)\n",startdiscard); abort(); } #endif flags >>= 1; high >>= 2; startdiscard++; } ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif if (flags) { /* return false; */ } for (i = 0; i < 16; i++) { *gbuffer++ = (unsigned char) (low & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 5\n"); abort(); } #endif low >>= 2; } for ( ; i < 32; i++) { *gbuffer++ = (unsigned char) (high & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 6\n"); abort(); } #endif high >>= 2; } ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif i = 0; while (i < enddiscard && i < 16) { if (flags & 0x01) { /* return false; */ } *gbuffer++ = (unsigned char) (low & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 7\n"); abort(); } #endif flags >>= 1; low >>= 2; i++; } while (i < enddiscard) { if (flags & 0x01) { /* return false; */ } *gbuffer++ = (unsigned char) (high & 0x03); #ifdef DEBUG3 if (check_nucleotide(gbuffer[k-1],gbuffer_debug[k-1])) { fprintf(stderr,"Case 8\n"); abort(); } #endif flags >>= 1; high >>= 2; i++; } } } return true; } #endif static void uncompress_mmap_nucleotides (unsigned char *gbuffer, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low; int startdiscard, enddiscard, i; ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; /* printf("startdiscard = %d, enddiscard = %d\n",startdiscard,enddiscard); */ if (endblock == startblock) { /* Special case */ if (startdiscard < 16) { #ifdef WORDS_BIGENDIAN low = Bigendian_convert_uint(blocks[ptr+1]); #else low = blocks[ptr+1]; #endif low >>= (startdiscard+startdiscard); while (startdiscard < enddiscard && startdiscard < 16) { *gbuffer++ = (unsigned char) (low & 0x03); low >>= 2; startdiscard++; } } if (enddiscard >= 16) { startdiscard -= 16; enddiscard -= 16; #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); #else high = blocks[ptr]; #endif high >>= (startdiscard+startdiscard); while (startdiscard < enddiscard) { *gbuffer++ = (unsigned char) (high & 0x03); high >>= 2; startdiscard++; } } } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); #else high = blocks[ptr]; low = blocks[ptr+1]; #endif if (startdiscard < 16) { low >>= (startdiscard+startdiscard); while (startdiscard < 16) { *gbuffer++ = (unsigned char) (low & 0x03); low >>= 2; startdiscard++; } } startdiscard -= 16; high >>= (startdiscard+startdiscard); while (startdiscard < 16) { *gbuffer++ = (unsigned char) (high & 0x03); high >>= 2; startdiscard++; } /* printf("Block %d assigned up to %d\n",ptr,k); */ ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); #else high = blocks[ptr]; low = blocks[ptr+1]; #endif for (i = 0; i < 16; i++) { *gbuffer++ = (unsigned char) (low & 0x03); low >>= 2; } for ( ; i < 32; i++) { *gbuffer++ = (unsigned char) (high & 0x03); high >>= 2; } /* printf("Block %d assigned up to %d\n",ptr,k); */ ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); #else high = blocks[ptr]; low = blocks[ptr+1]; #endif i = 0; while (i < enddiscard && i < 16) { *gbuffer++ = (unsigned char) (low & 0x03); low >>= 2; i++; } while (i < enddiscard) { *gbuffer++ = (unsigned char) (high & 0x03); high >>= 2; i++; } /* printf("Block %d assigned up to %d\n",ptr,k); */ } } #if 0 for (ptr = startpos, k = 0; ptr < endpos; ptr++, k++) { if (gbuffer[k] > 3) { printf("startpos = %u, endpos = %u, k = %d\n",startpos,endpos,k); printf("startblock %u, endblock %u\n",startblock,endblock); for (ptr = startpos, k = 0; ptr < endpos; ptr++, k++) { printf("%u %d %d\n",ptr,k,gbuffer[k]); } abort(); } } #endif return; } /* Assign A => 0, C => 1, G => 2, T => 3, N/X => 4 */ static void uncompress_mmap_int_string (unsigned char *gbuffer, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; int startdiscard, enddiscard, i; ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN flags = Bigendian_convert_uint(blocks[ptr+2]); #else flags = blocks[ptr+2]; #endif flags >>= startdiscard; if (startdiscard < 16) { #ifdef WORDS_BIGENDIAN low = Bigendian_convert_uint(blocks[ptr+1]); #else low = blocks[ptr+1]; #endif low >>= (startdiscard+startdiscard); while (startdiscard < enddiscard && startdiscard < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (low & 0x03); } low >>= 2; flags >>= 1; startdiscard++; } } if (enddiscard >= 16) { startdiscard -= 16; enddiscard -= 16; #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); #else high = blocks[ptr]; #endif high >>= (startdiscard+startdiscard); while (startdiscard < enddiscard) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (high & 0x03); } high >>= 2; flags >>= 1; startdiscard++; } } } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif flags >>= startdiscard; if (startdiscard < 16) { low >>= (startdiscard+startdiscard); while (startdiscard < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (low & 0x03); } low >>= 2; flags >>= 1; startdiscard++; } } startdiscard -= 16; high >>= (startdiscard+startdiscard); while (startdiscard < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (high & 0x03); } high >>= 2; flags >>= 1; startdiscard++; } /* printf("Block %d assigned up to %d\n",ptr,k); */ ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (low & 0x03); } low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (high & 0x03); } high >>= 2; flags >>= 1; } /* printf("Block %d assigned up to %d\n",ptr,k); */ ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif i = 0; while (i < enddiscard && i < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (low & 0x03); } low >>= 2; flags >>= 1; i++; } while (i < enddiscard) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = (unsigned char) (high & 0x03); } high >>= 2; flags >>= 1; i++; } /* printf("Block %d assigned up to %d\n",ptr,k); */ } } #if 0 for (ptr = startpos, k = 0; ptr < endpos; ptr++, k++) { if (gbuffer[k] > 3) { printf("startpos = %u, endpos = %u, k = %d\n",startpos,endpos,k); printf("startblock %u, endblock %u\n",startblock,endblock); for (ptr = startpos, k = 0; ptr < endpos; ptr++, k++) { printf("%u %d %d\n",ptr,k,gbuffer[k]); } abort(); } } #endif return; } static void uncompress_mmap_int_string_convert (unsigned char *gbuffer, Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos, unsigned char *conversion) { /* Chrpos_T length = endpos - startpos; */ Univcoord_T startblock, endblock, ptr; Genomecomp_T high, low, flags; int startdiscard, enddiscard, i; ptr = startblock = startpos/32U*3; endblock = endpos/32U*3; startdiscard = startpos % 32; enddiscard = endpos % 32; if (endblock == startblock) { /* Special case */ #ifdef WORDS_BIGENDIAN flags = Bigendian_convert_uint(blocks[ptr+2]); #else flags = blocks[ptr+2]; #endif flags >>= startdiscard; if (startdiscard < 16) { #ifdef WORDS_BIGENDIAN low = Bigendian_convert_uint(blocks[ptr+1]); #else low = blocks[ptr+1]; #endif low >>= (startdiscard+startdiscard); while (startdiscard < enddiscard && startdiscard < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (low & 0x03)]; } low >>= 2; flags >>= 1; startdiscard++; } } if (enddiscard >= 16) { startdiscard -= 16; enddiscard -= 16; #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); #else high = blocks[ptr]; #endif high >>= (startdiscard+startdiscard); while (startdiscard < enddiscard) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (high & 0x03)]; } high >>= 2; flags >>= 1; startdiscard++; } } } else { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif flags >>= startdiscard; if (startdiscard < 16) { low >>= (startdiscard+startdiscard); while (startdiscard < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (low & 0x03)]; } low >>= 2; flags >>= 1; startdiscard++; } } startdiscard -= 16; high >>= (startdiscard+startdiscard); while (startdiscard < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (high & 0x03)]; } high >>= 2; flags >>= 1; startdiscard++; } /* printf("Block %d assigned up to %d\n",ptr,k); */ ptr += 3; while (ptr < endblock) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif for (i = 0; i < 16; i++) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (low & 0x03)]; } low >>= 2; flags >>= 1; } for ( ; i < 32; i++) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (high & 0x03)]; } high >>= 2; flags >>= 1; } /* printf("Block %d assigned up to %d\n",ptr,k); */ ptr += 3; } if (enddiscard > 0) { #ifdef WORDS_BIGENDIAN high = Bigendian_convert_uint(blocks[ptr]); low = Bigendian_convert_uint(blocks[ptr+1]); flags = Bigendian_convert_uint(blocks[ptr+2]); #else high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2]; #endif i = 0; while (i < enddiscard && i < 16) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (low & 0x03)]; } low >>= 2; flags >>= 1; i++; } while (i < enddiscard) { if (flags & 0x01) { *gbuffer++ = (unsigned char) 4; } else { *gbuffer++ = conversion[(int) (high & 0x03)]; } high >>= 2; flags >>= 1; i++; } /* printf("Block %d assigned up to %d\n",ptr,k); */ } } #if 0 for (ptr = startpos, k = 0; ptr < endpos; ptr++, k++) { if (gbuffer[k] > 3) { printf("startpos = %u, endpos = %u, k = %d\n",startpos,endpos,k); printf("startblock %u, endblock %u\n",startblock,endblock); for (ptr = startpos, k = 0; ptr < endpos; ptr++, k++) { printf("%u %d %d\n",ptr,k,gbuffer[k]); } abort(); } } #endif return; } /************************************************************************ * Usage procedures ************************************************************************/ static T genome; static Genomecomp_T *genome_blocks; static T genomealt; static Genomecomp_T *genomealt_blocks; /* Can be equal to genome_blocks, but not NULL */ static Mode_T mode; static int circular_typeint = -1; static char *fwd_conversion; static char *rev_conversion; void Genome_setup (T genome_in, T genomealt_in, Mode_T mode_in, int circular_typeint_in) { genome = genome_in; genome_blocks = genome->blocks; if (genomealt_in == NULL) { genomealt = genome_in; genomealt_blocks = genome->blocks; } else { genomealt = genomealt_in; genomealt_blocks = genomealt->blocks; } mode = mode_in; if (mode == STANDARD) { fwd_conversion = "ACGT"; rev_conversion = "ACGT"; } else if (mode == CMET_STRANDED || mode == CMET_NONSTRANDED) { fwd_conversion = "ATGT"; rev_conversion = "ACAT"; } else if (mode == ATOI_STRANDED || mode == ATOI_NONSTRANDED) { fwd_conversion = "GCGT"; rev_conversion = "ACGC"; } else if (mode == TTOC_STRANDED || mode == TTOC_NONSTRANDED) { fwd_conversion = "ACGC"; rev_conversion = "GCGT"; } circular_typeint = circular_typeint_in; return; } void Genome_user_setup (Genomecomp_T *genome_blocks_in) { genome = (T) NULL; genome_blocks = genome_blocks_in; genomealt = (T) NULL; genomealt_blocks = genome_blocks_in; mode = STANDARD; return; } static const Except_T gbufferlen_error = { "Insufficient allocation" }; static bool fill_buffer (Chrnum_T *chrnum, int *nunknowns, T this, Univcoord_T left, Chrpos_T length, char *gbuffer1, Univ_IIT_T chromosome_iit, bool bitbybitp, const char defaultchars[], const char flagchars[]) { Chrnum_T chrnum_left, chrnum_right, chrnumi; Univcoord_T inbounds_low, inbounds_high, pos, low, high, maxoverlap, overlap; Chrpos_T chrlength; *nunknowns = 0; if (length == 0) { *chrnum = 0; return false; } /* Fix out of bounds resulting from negative numbers */ if (left + length < left) { debug(printf("Got negative left\n")); while (left != 0U) { *(gbuffer1++) = OUTOFBOUNDS; *nunknowns += 1; length--; left++; } } if (this->compressedp == false) { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif if (lseek(this->fd,left,SEEK_SET) < 0) { perror("Error in fill_buffer"); exit(9); } read(this->fd,gbuffer1,length); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { memcpy(gbuffer1,&(this->chars[left]),length*sizeof(char)); } } else { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif uncompress_fileio(gbuffer1,this,left,left+length,defaultchars,flagchars); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { if (bitbybitp == true) { uncompress_mmap_bitbybit(gbuffer1,this->blocks,left,left+length,defaultchars,flagchars); } else { Genome_uncompress_mmap(gbuffer1,this->blocks,left,left+length); } } } gbuffer1[length] = '\0'; debug(printf("Got sequence at %llu with length %u, forward\n",(unsigned long long) left,length)); /* Fix out of bounds resulting from crossing chromosomes */ if (chromosome_iit == NULL) { debug(printf("No chr info because chromosome_iit is null\n")); /* None provided, perhaps because aligning to user segment */ } else if ((chrnum_left = Univ_IIT_get_one(chromosome_iit,left,left)) == (chrnum_right = Univ_IIT_get_one(chromosome_iit,left+length-1U,left+length-1U))) { debug(printf("Chr at beginning = %d, at end = %d\n",chrnum_left,chrnum_right)); *chrnum = chrnum_left; /* Fix out of bounds resulting from going past last chromosome */ Univ_IIT_interval_bounds(&low,&high,&chrlength,chromosome_iit,chrnum_left,circular_typeint); if (left >= high) { for (pos = 0; pos < length; pos++) { gbuffer1[pos] = OUTOFBOUNDS; *nunknowns += 1; } } else if (left+length >= high) { for (pos = high-left; pos < length; pos++) { gbuffer1[pos] = OUTOFBOUNDS; *nunknowns += 1; } } } else { debug(printf("Chr at beginning = %d, at end = %d\n",chrnum_left,chrnum_right)); maxoverlap = 0; for (chrnumi = chrnum_left; chrnumi <= chrnum_right; chrnumi++) { Univ_IIT_interval_bounds(&low,&high,&chrlength,chromosome_iit,chrnumi,circular_typeint); if (left > low) { low = left; } if (left+length < high) { high = left+length; } if ((overlap = high - low) > maxoverlap) { *chrnum = chrnumi; maxoverlap = overlap; inbounds_low = low - left; inbounds_high = high - left; } } debug(printf("in-bounds at %llu..%llu\n",(unsigned long long) inbounds_low,(unsigned long long) inbounds_high)); for (pos = 0; pos < inbounds_low; pos++) { gbuffer1[pos] = OUTOFBOUNDS; *nunknowns += 1; } for (pos = inbounds_high; pos < length; pos++) { gbuffer1[pos] = OUTOFBOUNDS; *nunknowns += 1; } debug(printf("%s\n",gbuffer1)); } return true; } bool Genome_fill_buffer (Chrnum_T *chrnum, int *nunknowns, T this, Univcoord_T left, Chrpos_T length, char *gbuffer1, Univ_IIT_T chromosome_iit) { return fill_buffer(&(*chrnum),&(*nunknowns),this,left,length,gbuffer1,chromosome_iit, /*bitbybitp*/false,DEFAULT_CHARS,DEFAULT_FLAGS); } void Genome_fill_buffer_simple (T this, Univcoord_T left, Chrpos_T length, char *gbuffer1) { int delta, i; #if 0 assert(left + length >= left); #endif /* Fix out of bounds resulting from negative numbers */ if (left + length < left) { /* fprintf(stderr,"left %llu + length %u < left %llu\n",(unsigned long long) left,length,(unsigned long long) left); */ delta = -left; length -= delta; for (i = 0; i < delta; i++) { gbuffer1[i] = '*'; /* Don't use 'N', which works in dynamic programming */ } gbuffer1[i] = '\0'; gbuffer1 += delta; left = 0U; } if (length == 0) { return; } if (this->compressedp == false) { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif if (lseek(this->fd,left,SEEK_SET) < 0) { perror("Error in Genome_fill_buffer_simple"); exit(9); } read(this->fd,gbuffer1,length); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { memcpy(gbuffer1,&(this->chars[left]),length*sizeof(char)); } } else { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif uncompress_fileio(gbuffer1,this,left,left+length,global_chars,global_flags); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { #ifdef EXTRACT_GENOMICSEG uncompress_mmap_bitbybit(gbuffer1,this->blocks,left,left+length,DEFAULT_FLAGS,A_FLAGS); #else Genome_uncompress_mmap(gbuffer1,this->blocks,left,left+length); #endif } } gbuffer1[length] = '\0'; debug(printf("Got sequence at %llu with length %u, forward\n",(unsigned long long) left,length)); return; } void Genome_fill_buffer_convert_fwd (Univcoord_T left, Chrpos_T length, char *gbuffer1) { if (length > 0) { assert(left + length >= left); uncompress_mmap_bitbybit(gbuffer1,genome_blocks,left,left+length,fwd_conversion,X_FLAGS); } gbuffer1[length] = '\0'; return; } void Genome_fill_buffer_convert_rev (Univcoord_T left, Chrpos_T length, char *gbuffer1) { if (length > 0) { assert(left + length >= left); uncompress_mmap_bitbybit(gbuffer1,genome_blocks,left,left+length,rev_conversion,X_FLAGS); } gbuffer1[length] = '\0'; return; } void Genome_fill_buffer_blocks (Univcoord_T left, Chrpos_T length, char *gbuffer1) { if (length > 0) { assert(left + length >= left); #ifdef EXTRACT_GENOMICSEG uncompress_mmap_bitbybit(gbuffer1,genome_blocks,left,left+length,DEFAULT_CHARS,A_FLAGS); #else Genome_uncompress_mmap(gbuffer1,genome_blocks,left,left+length); #endif } gbuffer1[length] = '\0'; return; } void Genome_fill_buffer_blocks_noterm (Univcoord_T left, Chrpos_T length, char *gbuffer1, char *gbuffer2) { if (length > 0) { assert(left + length >= left); Genome_uncompress_mmap(gbuffer1,genome_blocks,left,left+length); uncompress_mmap_snps_subst(gbuffer2,genome_blocks,genomealt_blocks,left,left+length); } /* gbuffer1[length] = '\0'; */ return; } void Genome_fill_buffer_simple_alt (T genome, T genomealt, Univcoord_T left, Chrpos_T length, char *gbuffer1) { int delta, i; #if 0 assert(left + length >= left); #endif /* Fix out of bounds resulting from negative numbers */ if (left + length < left) { /* fprintf(stderr,"left %llu + length %u < left %llu\n",(unsigned long long) left,length,(unsigned long long) left); */ delta = -left; length -= delta; for (i = 0; i < delta; i++) { gbuffer1[i] = '*'; /* Don't use 'N', which works in dynamic programming */ } gbuffer1[i] = '\0'; gbuffer1 += delta; left = 0U; } if (length == 0) { return; } if (genomealt->compressedp == false) { if (genomealt->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&genomealt->read_mutex); #endif if (lseek(genomealt->fd,left,SEEK_SET) < 0) { perror("Error in gmap, Genome_get_segment"); exit(9); } read(genomealt->fd,gbuffer1,length); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&genomealt->read_mutex); #endif } else { memcpy(gbuffer1,&(genomealt->chars[left]),length*sizeof(char)); } } else { if (genomealt->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&genomealt->read_mutex); #endif uncompress_fileio(gbuffer1,genomealt,left,left+length,DEFAULT_CHARS,SNP_FLAGS); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&genomealt->read_mutex); #endif } else { uncompress_mmap_snps_subst(gbuffer1,genome->blocks,genomealt->blocks,left,left+length); } } gbuffer1[length] = '\0'; debug(printf("Got sequence at %llu with length %u, forward\n",(unsigned long long) left,length)); return; } void Genome_fill_buffer_nucleotides (T this, Univcoord_T left, Chrpos_T length, unsigned char *gbuffer) { if (length == 0) { return; } /* Fix out of bounds resulting from negative numbers */ #if 0 if (left + length < left) { fprintf(stderr,"left %u + length %u < left %u\n",left,length,left); abort(); } #else assert(left + length >= left); #endif if (this->compressedp == false) { fprintf(stderr,"Procedure Genome_fill_buffer_nucleotides not designed to work for non-compressed genomes\n"); exit(9); if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { memcpy(gbuffer,&(this->chars[left]),length*sizeof(char)); } } else { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif fprintf(stderr,"Procedure Genome_fill_buffer_nucleotides not designed to work under FILEIO access\n"); exit(9); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { uncompress_mmap_nucleotides(gbuffer,this->blocks,left,left+length); } } gbuffer[length] = 0xFF; #if 0 for (i = 0; i <= length; i++) { printf("%d ",gbuffer[i]); } printf("\n"); #endif return; } void Genome_fill_buffer_int_string (T this, Univcoord_T left, Chrpos_T length, unsigned char *gbuffer, unsigned char *conversion) { if (length == 0) { return; } /* Fix out of bounds resulting from negative numbers */ #if 0 if (left + length < left) { fprintf(stderr,"left %u + length %u < left %u\n",left,length,left); abort(); } #else assert(left + length >= left); #endif if (this->compressedp == false) { fprintf(stderr,"Procedure Genome_fill_buffer_nucleotides not designed to work for non-compressed genomes\n"); exit(9); if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { memcpy(gbuffer,&(this->chars[left]),length*sizeof(char)); } } else { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif fprintf(stderr,"Procedure Genome_fill_buffer_nucleotides not designed to work under FILEIO access\n"); exit(9); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else if (conversion == NULL) { uncompress_mmap_int_string(gbuffer,this->blocks,left,left+length); } else { uncompress_mmap_int_string_convert(gbuffer,this->blocks,left,left+length,conversion); } } gbuffer[length] = 0xFF; #if 0 for (i = 0; i <= length; i++) { printf("%d ",gbuffer[i]); } printf("\n"); #endif return; } char Genome_get_char (T this, Univcoord_T left) { char c; char gbuffer1[1]; /* assert(left < 4000000000U); */ if (this->compressedp == false) { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif if (lseek(this->fd,left,SEEK_SET) < 0) { perror("Error in Genome_get_char"); exit(9); } read(this->fd,gbuffer1,/*length*/1); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { memcpy(gbuffer1,&(this->chars[left]),sizeof(char)); } } else { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif uncompress_fileio(gbuffer1,this,left,left+1,global_chars,global_flags); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { c = uncompress_one_char(this->blocks,left,/*flagchar*/'N',CHARTABLE); #ifdef EXTRACT_GENOMICSEG Genome_uncompress_mmap(gbuffer1,this->blocks,left,left+1); assert(c == gbuffer1[0]); #endif return c; } } return gbuffer1[0]; } /* Removed checks for uncompressed genome and fileio access */ char Genome_get_char_lex (T this, Univcoord_T left, Univcoord_T genomelength, char chartable[]) { #ifdef EXTRACT_GENOMICSEG char c; char gbuffer1[1]; #endif /* assert(left < 4000000000U); */ if (left >= genomelength) { return (char) 0; } else { #ifdef EXTRACT_GENOMICSEG Genome_uncompress_mmap(gbuffer1,this->blocks,left,left+1); assert(c == gbuffer1[0]); return c; #else /* Want 'X', because in building suffix array, the encoding was A(0), C(1), G(2), T(3), N(4) */ return uncompress_one_char(this->blocks,left,/*flagchar*/'X',chartable); #endif } } char Genome_get_char_blocks (char *charalt, Univcoord_T left) { char c; #ifdef EXTRACT_GENOMICSEG char gbuffer1[1]; #endif /* assert(left < 4000000000U); */ /* printf("Genome_get_char_blocks called with left = %u\n",left); */ if ((c = uncompress_one_char(genome_blocks,left,/*flagchar*/'N',CHARTABLE)) == 'N') { *charalt = c; } else { *charalt = uncompress_one_char_ignore_flags(genomealt_blocks,left); } #ifdef EXTRACT_GENOMICSEG Genome_uncompress_mmap(gbuffer1,genome_blocks,left,left+1); assert(c == gbuffer1[0]); #endif return c; } void Genome_get_segment_blocks_right (char *segment, char *segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chrhigh, bool revcomp) { Chrpos_T out_of_bounds, i; if (length == 0) { segment[0] = segmentalt[0] = '\0'; return; } else if (left >= chrhigh) { /* All out of bounds */ segment[0] = segmentalt[0] = '\0'; return; } else if (left + length >= chrhigh) { out_of_bounds = left + length - chrhigh; /* Cannot check i >= length - out_of_bounds when i is unsigned */ for (i = length - 1; i + out_of_bounds >= length; i--) { segment[i] = '*'; } } else { out_of_bounds = 0; } /* printf("Genome_get_segment_blocks called with left = %u, revcomp %d\n",left,revcomp); */ Genome_uncompress_mmap(segment,genome_blocks,left,left+length-out_of_bounds); segment[length] = '\0'; if (revcomp == true) { make_complement_inplace(segment,length); } if (genomealt_blocks == genome_blocks) { strncpy(segmentalt,segment,length); segmentalt[length] = '\0'; } else { for (i = length - 1; i >= length - out_of_bounds; i--) { segmentalt[i] = '*'; } uncompress_mmap_snps_subst(segmentalt,genome_blocks,genomealt_blocks,left,left+length-out_of_bounds); segmentalt[length] = '\0'; if (revcomp == true) { make_complement_inplace(segmentalt,length); } } return; } /* Note: Must call this function with the right coordinate (left + length), not the left coordinate */ void Genome_get_segment_blocks_left (char *segment, char *segmentalt, Univcoord_T right, Chrpos_T length, Univcoord_T chroffset, bool revcomp) { Chrpos_T out_of_bounds, i; if (length == 0) { segment[0] = segmentalt[0] = '\0'; return; } else if (right < chroffset) { /* All out of bounds */ segment[0] = segmentalt[0] = '\0'; return; } else if (right < chroffset + length) { out_of_bounds = chroffset + length - right; for (i = 0; i < out_of_bounds; i++) { segment[i] = '*'; } } else { out_of_bounds = 0; } /* printf("Genome_get_segment_blocks called with left = %u, revcomp %d\n",right-length,revcomp); */ Genome_uncompress_mmap(&(segment[out_of_bounds]),genome_blocks,right-length+out_of_bounds,right); segment[length] = '\0'; if (revcomp == true) { make_complement_inplace(segment,length); } if (genomealt_blocks == genome_blocks) { strncpy(segmentalt,segment,length); segmentalt[length] = '\0'; } else { for (i = 0; i < out_of_bounds; i++) { segmentalt[i] = '*'; } uncompress_mmap_snps_subst(&(segmentalt[out_of_bounds]),genome_blocks,genomealt_blocks,right-length+out_of_bounds,right); segmentalt[length] = '\0'; if (revcomp == true) { make_complement_inplace(segmentalt,length); } } return; } bool buffers_diff_p (char *buffer1, char *buffer2, int length) { int i; for (i = 0; i < length; i++) { if (buffer1[i] != buffer2[i]) { return true; } } return false; } Sequence_T Genome_get_segment (T this, Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit, bool revcomp) { Chrnum_T chrnum; int nunknowns; char *gbuffer; gbuffer = (char *) MALLOC_IN((length+1)*sizeof(char)); fill_buffer(&chrnum,&nunknowns,this,left,length,gbuffer,chromosome_iit, /*bitbybitp*/false,DEFAULT_CHARS,DEFAULT_FLAGS); if (revcomp == true) { /* make_complement_buffered(gbuffer2,gbuffer1,length);*/ make_complement_inplace(gbuffer,length); debug(printf("Got sequence at %llu with length %u, revcomp\n",(unsigned long long) left,length)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer,length,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer,length,/*copyp*/false); } else { debug(printf("Got sequence at %llu with length %u, forward\n",(unsigned long long) left,length)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer,length,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer,length,/*copyp*/false); } } Sequence_T Genome_get_segment_alt (T this, Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit, bool revcomp) { Chrnum_T chrnum; int nunknowns; char *gbuffer; gbuffer = (char *) MALLOC_IN((length+1)*sizeof(char)); fill_buffer(&chrnum,&nunknowns,this,left,length,gbuffer,chromosome_iit, /*bitbybitp*/true,DEFAULT_CHARS,SNP_FLAGS); if (revcomp == true) { /* make_complement_buffered(gbuffer2,gbuffer1,length); */ make_complement_inplace(gbuffer,length); debug(printf("Got sequence at %llu with length %u, revcomp\n",(unsigned long long) left,length)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer,length,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer,length,/*copyp*/false); } else { debug(printf("Got sequence at %llu with length %u, forward\n",(unsigned long long) left,length)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer1,length,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer,length,/*copyp*/false); } } Sequence_T Genome_get_segment_snp (T this, Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit, bool revcomp) { Chrnum_T chrnum; int nunknowns; char *gbuffer; gbuffer = (char *) MALLOC_IN((length+1)*sizeof(char)); fill_buffer(&chrnum,&nunknowns,this,left,length,gbuffer,chromosome_iit, /*bitbybitp*/true,SNP_CHARS,SNP_FLAGS); if (revcomp == true) { /* make_complement_buffered(gbuffer2,gbuffer1,length); */ make_complement_inplace(gbuffer,length); debug(printf("Got sequence at %llu with length %u, revcomp\n",(unsigned long long) left,length)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer,length,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer,length,/*copyp*/false); } else { debug(printf("Got sequence at %llu with length %u, forward\n",(unsigned long long) left,length)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer,length,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer,length,/*copyp*/false); } } Univcoord_T Genome_ntcounts (Univcoord_T *na, Univcoord_T *nc, Univcoord_T *ng, Univcoord_T *nt, T this, Univcoord_T left, Univcoord_T length) { char *gbuffer, *p; Univcoord_T i; *na = *nc = *ng = *nt = 0; if (length == 0) { return 0; } /* Fix out of bounds resulting from negative numbers */ #if 0 if (left + length < left) { fprintf(stderr,"left %u + length %u < left %u\n",left,length,left); abort(); } #else assert(left + length >= left); #endif if (this->compressedp == false) { if (this->access == FILEIO) { gbuffer = (char *) CALLOC(length,sizeof(char)); #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif if (lseek(this->fd,left,SEEK_SET) < 0) { perror("Error in gmap, Genome_get_segment"); exit(9); } read(this->fd,gbuffer,length); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif p = &(gbuffer[0]); for (i = 0; i < length; i++) { switch (*p) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } p++; } FREE(gbuffer); } else { p = &(this->chars[left]); for (i = 0; i < length; i++) { switch (*p) { case 'A': case 'a': (*na)++; break; case 'C': case 'c': (*nc)++; break; case 'G': case 'g': (*ng)++; break; case 'T': case 't': (*nt)++; break; } p++; } } } else { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif ntcounts_fileio(&(*na),&(*nc),&(*ng),&(*nt), this,left,left+length,global_chars,global_flags); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { Genome_ntcounts_mmap(&(*na),&(*nc),&(*ng),&(*nt), this->blocks,left,left+length,global_chars,global_flags); } } debug(printf("Got sequence at %llu with length %u, forward\n",(unsigned long long) left,length)); return (*na) + (*nc) + (*ng) + (*nt); } #if 0 int Genome_next_char (T this) { char gbuffer[2]; if (this->compressedp == false) { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif read(this->fd,gbuffer,1); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif return (int) gbuffer[0]; } else { return *(this->ptr++); } } else { if (this->access == FILEIO) { #ifdef HAVE_PTHREAD pthread_mutex_lock(&this->read_mutex); #endif uncompress_fileio(gbuffer,this,this->left,this->left+1U,DEFAULT_CHARS,DEFAULT_FLAGS); #ifdef HAVE_PTHREAD pthread_mutex_unlock(&this->read_mutex); #endif } else { Genome_uncompress_mmap(gbuffer,this->blocks,this->left,this->left+1U); } this->left += 1U; return (int) gbuffer[0]; } } #endif #if 0 /* sbuffer is the strain buffer, with coordinates low--high. gbuffer1 has the reference sequence in the forward direction. The reference sequence has coordinates left + length. The calling procedure has ordered the indices in descending genomic position, so that right shifting works. */ Sequence_T Genome_patch_strain (int *indices, int nindices, IIT_T altstrain_iit, Chrpos_T refL, Chrpos_T reflen, bool revcomp, char *gbuffer1, char *gbuffer2, char *gbuffer3, int gbuffer3len) { Chrpos_T refR, srcL, srcR, matR; Interval_T interval; char *dest, *src, *matbuffer, *shiftdest, *shiftsrc, *restofheader; int index, i, matlen, patchlen, shiftlen, expansion; bool allocp; assert(reflen <= gbuffer3len); refR = refL + reflen; debug2(printf("refL=%u refR=%u reflen=%u\n",refL,refR,reflen)); /* Work in gbuffer3 */ memcpy(gbuffer3,gbuffer1,reflen); for (i = 0; i < nindices; i++) { index = indices[i]; interval = IIT_interval(altstrain_iit,index); srcL = Interval_low(interval); srcR = Interval_high(interval) + 1; /* Intervals are inclusive */ matbuffer = IIT_annotation(&restofheader,altstrain_iit,index,&allocp); /* Holds the sequence */ matlen = IIT_annotation_strlen(altstrain_iit,index); matR = srcL + matlen; /* Truncate srcR and matR */ if (srcR > refR) { srcR = refR; } if (matR > refR) { matR = refR; } expansion = matR - srcR; /* Find dest and src */ if (srcL < refL) { dest = &(gbuffer3[0]); src = &(matbuffer[refL-srcL]); patchlen = matR - refL; } else { dest = &(gbuffer3[srcL-refL]); src = &(matbuffer[0]); patchlen = matR - srcL; } if (allocp == true) { FREE(restofheader); } debug2(printf("srcL=%u matR=%u srcR=%u matlen=%u patchlen=%d expansion=%d\n", srcL,matR,srcR,matlen,patchlen,expansion)); /* If patchlen < 0, then matR is to left of refL and we are done */ if (patchlen > 0) { memcpy(dest,src,patchlen*sizeof(char)); if (expansion < 0) { /* Contraction: shouldn't occur because gmapindex will fill in with x's */ dest += patchlen; while (expansion < 0) { *dest++ = 'x'; expansion++; } } else if (expansion > 0) { dest += patchlen; src += patchlen; shiftlen = refR - matR - expansion; shiftsrc = dest; shiftdest = shiftsrc + expansion; memmove(shiftdest,shiftsrc,shiftlen*sizeof(char)); memcpy(dest,src,expansion*sizeof(char)); debug2(printf(" shifted %d\n",shiftlen)); } } } debug2(printf("\n")); if (revcomp == true) { make_complement_buffered(gbuffer2,gbuffer3,reflen); /* FREE(sequence); */ debug(printf("Got sequence at %u with length %u, revcomp\n",refL,reflen)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer2,reflen,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer2,reflen,/*copyp*/false); } else { debug(printf("Got sequence at %u with length %u, forward\n",refL,reflen)); debug1(Sequence_print(stdout,Sequence_genomic_new(gbuffer3,reflen,/*copyp*/false),false,60,true)); return Sequence_genomic_new(gbuffer3,reflen,/*copyp*/false); } } #endif