/* Obscure.h - stuff that's relatively rarely used * but still handy. * * This file is copyright 2002 Jim Kent, but license is hereby * granted for all use - public, private or commercial. */ #ifndef OBSCURE_H #define OBSCURE_H long incCounterFile(char *fileName); /* Increment a 32 bit value on disk. */ int digitsBaseTwo(unsigned long x); /* Return base two # of digits. */ int digitsBaseTen(int x); /* Return number of digits base 10. */ void sprintLongWithCommas(char *s, long long l); /* Print out a long number with commas a thousands, millions, etc. */ void printLongWithCommas(FILE *f, long long l); /* Print out a long number with commas a thousands, millions, etc. */ void sprintWithGreekByte(char *s, int slength, long long size); /* Numbers formatted with PB, TB, GB, MB, KB, B */ void printWithGreekByte(FILE *f, long long l); /* Print with formatting in gigabyte, terabyte, etc. */ void sprintWithMetricBaseUnit(char *s, int slength, long long size); /* Numbers formatted with Pb, Tb, Gb, Mb, kb, bp */ void printWithMetricBaseUnit(FILE *f, long long l); /* Print with formatting in megabase, kilobase, etc. */ void writeGulp(char *file, char *buf, int size); /* Write out a bunch of memory. */ void readInGulp(char *fileName, char **retBuf, size_t *retSize); /* Read whole file in one big gulp. */ void readAllWords(char *fileName, char ***retWords, int *retWordCount, char **retBuf); /* Read in whole file and break it into words. You need to freeMem both * *retWordCount and *retBuf when done. */ int countWordsInFile(char *fileName); /* Count number of words in file. */ struct slName *readAllLines(char *fileName); /* Read all lines of file into a list. (Removes trailing carriage return.) */ void copyFile(char *source, char *dest); /* Copy file from source to dest. */ void copyOpenFile(FILE *inFh, FILE *outFh); /* copy an open stdio file */ void cpFile(int s, int d); /* Copy from source file to dest until reach end of file. */ void *charToPt(char c); /* Convert char to pointer. Use when really want to store * a char in a pointer field. */ char ptToChar(void *pt); /* Convert pointer to char. Use when really want to store a * pointer in a char. */ void *intToPt(int i); /* Convert integer to pointer. Use when really want to store an * int in a pointer field. */ int ptToInt(void *pt); /* Convert pointer to integer. Use when really want to store a * pointer in an int. */ void *sizetToPt(size_t i); /* Convert size_t to pointer. Use when really want to store a * size_t in a pointer. */ size_t ptToSizet(void *pt); /* Convert pointer to size_t. Use when really want to store a * pointer in a size_t. */ boolean parseQuotedStringNoEscapes( char *in, char *out, char **retNext); /* Read quoted string from in (which should begin with first quote). * Write unquoted string to out, which may be the same as in. * Return pointer to character past end of string in *retNext. * Return FALSE if can't find end. * Unlike parseQuotedString() do not treat backslash as an escape * character, merely pass it on through. */ boolean parseQuotedString( char *in, char *out, char **retNext); /* Read quoted string from in (which should begin with first quote). * Write unquoted string to out, which may be the same as in. * Return pointer to character past end of string in *retNext. * Return FALSE if can't find end. */ char *nextQuotedWord(char **pLine); /* Generalization of nextWord. Returns next quoted * string or if no quotes next word. Updates *pLine * to point past word that is returned. Does not return * quotes. */ struct slName *slNameListOfUniqueWords(char *text,boolean respectQuotes); /* Return list of unique words found by parsing string delimited by whitespace. * If respectQuotes then ["Lucy and Ricky" 'Fred and Ethyl'] will yield 2 slNames no quotes */ char *makeQuotedString(char *in, char quoteChar); /* Create a string surrounded by quoteChar, with internal * quoteChars escaped. freeMem result when done. */ char *makeEscapedString(char *in, char toEscape); /* Return string that is a copy of in, but with all * toEscape characters preceded by '\' * When done freeMem result. */ void escCopy(char *in, char *out, char toEscape, char escape); /* Copy in to out, escaping as needed. Out better be big enough. * (Worst case is strlen(in)*2 + 1.) */ struct slName *stringToSlNames(char *string); /* Convert string to a list of slNames separated by * white space, but allowing multiple words in quotes. * Quotes if any are stripped. */ struct slName *commaSepToSlNames(char *commaSep); /* Convert comma-separated list of items to slName list. */ struct slName *charSepToSlNames(char *string, char c); /* Convert character-separated list of items to slName list. * Note that the last occurence of c is optional. (That * is for a comma-separated list a,b,c and a,b,c, are * equivalent. */ struct hash *hashVarLine(char *line, int lineIx); /* Return a symbol table from a line of form: * var1=val1 var2='quoted val2' var3="another val" */ struct hash *hashThisEqThatLine(char *line, int lineIx, boolean firstStartsWithLetter); /* Return a symbol table from a line of form: * 1-this1=val1 2-this='quoted val2' var3="another val" * If firstStartsWithLetter is true, then the left side of the equals must start with * and equals. */ struct hash *hashWordsInFile(char *fileName, int hashSize); /* Create a hash of space delimited words in file. * hashSize is as in hashNew() - pass 0 for default. */ struct hash *hashNameIntFile(char *fileName); /* Given a two column file (name, integer value) return a * hash keyed by name with integer values */ struct hash *hashTwoColumnFile(char *fileName); /* Given a two column file (key, value) return a hash. */ struct hash *hashTsvBy(char *in, int keyColIx, int *retColCount); /* Return a hash of rows keyed by the given column */ void writeTsvRow(FILE *f, int rowSize, char **row); /* Write out row of strings to a line in tab-sep file */ struct slPair *slPairTwoColumnFile(char *fileName); /* Read in a two column file into an slPair list */ void shuffleArrayOfChars(char *array, int arraySize); /* Shuffle array of characters of given size given number of times. */ void shuffleArrayOfInts(int *array, int arraySize); /* Shuffle array of ints of given size given number of times. */ void shuffleArrayOfPointers(void *pointerArray, int arraySize); /* Shuffle array of pointers of given size given number of times. */ void shuffleList(void *pList); /* Randomize order of slList. Usage: * shuffleList(&list) * where list is a pointer to a structure that * begins with a next field. */ void *slListRandomReduce(void *list, double reduceRatio); /* Reduce list to approximately reduceRatio times original size. Destroys original list. */ void *slListRandomSample(void *list, int maxCount); /* Return a sublist of list with at most maxCount. Destroy list in process */ char *stripCommas(char *position); /* make a new string with commas stripped out */ void dotForUserInit(int dotMod); /* Set how often dotForUser() outputs a dot. */ void dotForUser(); /* Write out a dot every _dotForUserMod times this is called. */ void dotForUserEnd(); /* Write out new line at end of dots for user */ void spaceToUnderbar(char *s); /* Convert white space to underbar. */ void rangeRoundUp(double start, double end, double *retStart, double *retEnd); /* Round start and end so that they cover a slightly bigger range, but with more round * numbers. For instance 0.23:9.89 becomes 0:10 */ void rangeFromMinMaxMeanStd(double minVal, double maxVal, double mean, double std, double *retStart, double *retEnd); /* Given some basic statistical properties, set a range that will be good on a wide * range of biological data. */ long long currentVmPeak(); /* return value of peak Vm memory usage (if /proc/ business exists) */ void printVmPeak(); /* print to stderr peak Vm memory usage (if /proc/ business exists) */ boolean nameInCommaList(char *name, char *commaList); /* Return TRUE if name is in comma separated list. */ boolean endsWithWordComma(char *string, char *word); /* Return TRUE if string ends with word possibly followed by a comma, and the beginning * of word within string is the beginning of string or follows a comma. */ void ensureNamesCaseUnique(struct slName *fieldList); /* Ensure that there would be no name conflicts in fieldList if all fields were lower-cased. */ boolean readAndIgnore(char *fileName); /* Read a byte from fileName, so its access time is updated. */ int get_thread_id(); /* return an integer specific for the current thread */ #endif /* OBSCURE_H */