/* pslReps - analyse repeats and generate list of best alignments
 * from a genome wide, sorted by mRNA .psl alignment file.
 */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "memalloc.h"
#include "psl.h"
#include "options.h"
#include "obscure.h"
#include "sqlNum.h"


/* command line */
static struct optionSpec optionSpecs[] = {
    {"minAli", OPTION_FLOAT},
    {"nearTop", OPTION_FLOAT},
    {"minCover", OPTION_FLOAT},
    {"minNearTopSize", OPTION_INT},
    {"ignoreSize", OPTION_BOOLEAN},
    {"sizeMatters", OPTION_BOOLEAN},  /* opposite of ignore size, for compat */
    {"noIntrons", OPTION_BOOLEAN},
    {"singleHit", OPTION_BOOLEAN},
    {"nohead", OPTION_BOOLEAN},
    {"ignoreNs", OPTION_BOOLEAN},
    {"coverQSizes", OPTION_STRING},
    {NULL, 0}
};

double minAli = 0.93;
double nearTop = 0.01;
double minCover = 0.0;
boolean ignoreNs = FALSE; /* Ignore the n's when calculating coverage score, other
			     wise n's count as mismatches. */
boolean ignoreSize = FALSE;
boolean noIntrons = FALSE;
boolean singleHit = FALSE;
boolean noHead = FALSE;
boolean quiet = FALSE;
int minNearTopSize = 30;
char *coverQSizeFile = NULL;

void usage()
/* Print usage instructions and exit. */
{
errAbort(
    "pslReps - Analyze repeats and generate genome-wide best alignments from a\n"
    "sorted set of local alignments\n"
    "usage:\n"
    "    pslReps in.psl out.psl out.psr\n"
    "where:\n"
    "    in.psl is an alignment file generated by psLayout and sorted by pslSort\n" 
    "    out.psl is the best alignment output\n"
    "    out.psr contains repeat info\n"
    "options:\n"
    "    -nohead            Don't add PSL header.\n"
    "    -ignoreSize        Will not weigh as much in favor of larger alignments.\n"
    "    -noIntrons         Will not penalize for not having introns when calculating\n"
    "                       size factor.\n"
    "    -singleHit         Takes single best hit, not splitting into parts.\n"
    "    -minCover=0.N      Minimum coverage to output.  Default is 0.\n"
    "    -ignoreNs          Ignore Ns when calculating minCover.\n"
    "    -minAli=0.N        Minimum alignment ratio.  Default is 0.93.\n"
    "    -nearTop=0.N       How much can deviate from top and be taken.\n"
    "                       Default is 0.01.\n"
    "    -minNearTopSize=N  Minimum size of alignment that is near top\n"
    "                       for alignment to be kept.  Default 30.\n"
    "    -coverQSizes=file  Tab-separate file with effective query sizes.\n"
    "                       When used with -minCover, this allows polyAs\n"
    "                       to be excluded from the coverage calculation.\n");
}

/* hash table of query name to sizes */
struct hash* coverQSizes = NULL;

void loadCoverQSizes(char* coverQSizeFile)
/* load coverage query sizes */
{
struct lineFile *lf = lineFileOpen(coverQSizeFile, TRUE);
char *row[2];
coverQSizes = hashNew(0);

while (lineFileNextRowTab(lf, row, ArraySize(row)))
    {
    int qSize = sqlSigned(row[1]);
    hashAdd(coverQSizes, row[0], intToPt(qSize));
    }

lineFileClose(&lf);
}

int calcMilliScore(struct psl *psl)
/* Figure out percentage score. */
{
return 1000-pslCalcMilliBad(psl, TRUE);
}

int intronFactor(struct psl *psl)
/* Figure bonus for having introns.  An intron is worth 3 bases... 
 * An intron in this case is just a gap of 0 bases in query and
 * 30 or more in target. */
{
int i, blockCount = psl->blockCount;
int ts, qs, te, qe, sz;
int bonus = 0;
if (blockCount <= 1)
    return 0;
sz = psl->blockSizes[0];
qe = psl->qStarts[0] + sz;
te = psl->tStarts[0] + sz;
for (i=1; i<blockCount; ++i)
    {
    qs = psl->qStarts[i];
    ts = psl->tStarts[i];
    if (qs == qe && ts - te >= 30)
        bonus += 3;
    sz = psl->blockSizes[i];
    qe = qs + sz;
    te = ts + sz;
    }
if (bonus > 10) bonus = 10;
return bonus;
}

int sizeFactor(struct psl *psl)
/* Return a factor that will favor longer alignments. */
{
int score;
if (ignoreSize) return 0;
score = 4*round(sqrt(psl->match + psl->repMatch/4));
if (!noIntrons)
    score += intronFactor(psl);
return score;
}

int calcSizedScore(struct psl *psl)
/* Return score that includes base matches and size. */
{
int score = calcMilliScore(psl) + sizeFactor(psl);
return score;
}

boolean uglyTarget(struct psl *psl)
/* Return TRUE if it's the one we're snooping on. */
{
return sameString(psl->qName, "AF103731");
}


boolean closeToTop(struct psl *psl, int *scoreTrack)
/* Returns TRUE if psl is near the top scorer for at least 20 bases. */
{
int milliScore = calcSizedScore(psl);
int threshold = round(milliScore * (1.0+nearTop));
int i, blockIx;
int start, size, end;
int topCount = 0;
char strand = psl->strand[0];

for (blockIx = 0; blockIx < psl->blockCount; ++blockIx)
    {
    start = psl->qStarts[blockIx];
    size = psl->blockSizes[blockIx];
    end = start+size;
    if (strand == '-')
	reverseIntRange(&start, &end, psl->qSize);
    for (i=start; i<end; ++i)
	{
	if (scoreTrack[i] <= threshold)
	    {
	    if (++topCount >= minNearTopSize)
		return TRUE;
	    }
	}
    }
return FALSE;
}

boolean passMinCoverage(struct psl *psl)
/* Does this psl have enough bases aligned to pass the minCover filter. */
{
int qSize = psl->qSize;
if (coverQSizes != NULL)
    {
    struct hashEl *hel = hashLookup(coverQSizes, psl->qName);
    if (hel != NULL)
        qSize = ptToInt(hel->val);
    }

if(ignoreNs)
    return (psl->match + psl->repMatch >= minCover * (qSize - psl->nCount));
else
    return (psl->match + psl->repMatch >= minCover * qSize);
}

boolean passFilters(struct psl *psl, int *scoreTrack)
/* Return TRUE if this psl passes the millScore, minCoverage and
   closeToTop thresholds.  If scoreTrack is NULL then closeToTop
   threshold is skipped. */
{
int milliMin = 1000*minAli;
if (calcMilliScore(psl) >= milliMin && 
    (scoreTrack == NULL || closeToTop(psl, scoreTrack)) &&
    passMinCoverage(psl))
    return TRUE;
return FALSE;
}

void processBestMulti(char *acc, struct psl *pslList, FILE *bestFile, FILE *repFile)
/* Find psl's that are best anywhere along their length. */
{
struct psl *psl;
int qSize;
int *repTrack = NULL;
int *scoreTrack = NULL;
int milliScore;
int goodAliCount = 0;
int bestAliCount = 0;
int milliMin = 1000*minAli;


if (pslList == NULL)
    return;
qSize = pslList->qSize;
AllocArray(repTrack, qSize+1);
AllocArray(scoreTrack, qSize+1);

for (psl = pslList; psl != NULL; psl = psl->next)
    {
    int blockIx;
    char strand = psl->strand[0];
    milliScore = calcMilliScore(psl);
    if (milliScore >= milliMin)
	{
	++goodAliCount;
	milliScore += sizeFactor(psl);
	for (blockIx = 0; blockIx < psl->blockCount; ++blockIx)
	    {
	    int start = psl->qStarts[blockIx];
	    int size = psl->blockSizes[blockIx];
	    int end = start+size;
	    int i;
	    if (strand == '-')
	        reverseIntRange(&start, &end, psl->qSize);
	    if (start < 0 || end > qSize)
		{
		warn("Odd: qName %s tName %s qSize %d psl->qSize %d start %d end %d",
		    psl->qName, psl->tName, qSize, psl->qSize, start, end);
		if (start < 0)
		    start = 0;
		if (end > qSize)
		    end = qSize;
		}
	    for (i=start; i<end; ++i)
		{
		repTrack[i] += 1;
		if (milliScore > scoreTrack[i])
		    scoreTrack[i] = milliScore;
		}
	    }
	}
    }
/* Print out any alignments that are within 2% of top score. */
for (psl = pslList; psl != NULL; psl = psl->next)
    {
    if(passFilters(psl, scoreTrack))
	{
	pslTabOut(psl, bestFile);
	++bestAliCount;
	}
    }


/* Print out run-length-encoded repeat info.  */
    {
    int runVal = repTrack[0];
    int curVal;
    int runSize = 1;
    int packetCount = 0;
    int *packetSize = NULL;
    int *packetVal = NULL;
    int i;

    AllocArray(packetSize, qSize);
    AllocArray(packetVal, qSize);

    repTrack[qSize] = -1;	/* Sentinal value to simplify RLC loop. */
    fprintf(repFile, "%s\t%d\t%d\t", acc, bestAliCount, goodAliCount);

    for (i=1; i<=qSize; ++i)
	{
	if ((curVal = repTrack[i]) != runVal)
	    {
	    packetSize[packetCount] = runSize;
	    packetVal[packetCount] = runVal;
	    ++packetCount;
	    runSize = 1;
	    runVal = curVal;
	    }
	else
	    {
	    ++runSize;
	    }
	}
    fprintf(repFile, "%d\t", packetCount);
    for (i=0; i<packetCount; ++i)
	fprintf(repFile, "%d,", packetSize[i]);
    fprintf(repFile, "\t");
    for (i=0; i<packetCount; ++i)
	fprintf(repFile, "%d,", packetVal[i]);
    fprintf(repFile, "\n");

    freeMem(packetSize);
    freeMem(packetVal);
    }

freeMem(repTrack);
freeMem(scoreTrack);
}

void processBestSingle(char *acc, struct psl *pslList, FILE *bestFile, FILE *repFile)
/* Find single best psl in list. */
{
struct psl *psl;
int bestScore = 0, score, threshold;

for (psl = pslList; psl != NULL; psl = psl->next)
    {
    score = pslScore(psl);
    if (score > bestScore)
	bestScore = score;
    }
threshold = round((1.0 - nearTop)*bestScore);
for (psl = pslList; psl != NULL; psl = psl->next)
    {
    if (pslScore(psl) >= threshold && passFilters(psl, NULL))
        pslTabOut(psl, bestFile);
    }
}

void doOneAcc(char *acc, struct psl *pslList, FILE *bestFile, FILE *repFile)
/* Process alignments of one piece of mRNA. */
{
if (singleHit)
    processBestSingle(acc, pslList, bestFile, repFile);
else
    processBestMulti(acc, pslList, bestFile, repFile);
}

void pslReps(char *inName, char *bestAliName, char *repName)
/* Analyse inName and put best alignments for eacmRNA in estAliName.
 * Put repeat info in repName. */
{
struct lineFile *in = pslFileOpen(inName);
FILE *bestFile = mustOpen(bestAliName, "w");
FILE *repFile = mustOpen(repName, "w");
int lineSize;
char *line;
char *words[32];
int wordCount;
struct psl *pslList = NULL, *psl = NULL;
char lastName[512];
int aliCount = 0;
quiet = sameString(bestAliName, "stdout") || sameString(repName, "stdout");
if (coverQSizeFile != NULL)
    loadCoverQSizes(coverQSizeFile);

if (!quiet)
    printf("Processing %s to %s and %s\n", inName, bestAliName, repName);
 if (!noHead)
     pslWriteHead(bestFile);
strcpy(lastName, "");
while (lineFileNext(in, &line, &lineSize))
    {
    if (((++aliCount & 0x1ffff) == 0) && !quiet)
        {
	printf(".");
	fflush(stdout);
	}
    wordCount = chopTabs(line, words);
    if (wordCount == 21)
	psl = pslLoad(words);
    else if (wordCount == 23)
	psl = pslxLoad(words);
    else
	errAbort("Bad line %d of %s\n", in->lineIx, in->fileName);
    if (!sameString(lastName, psl->qName))
	{
	doOneAcc(lastName, pslList, bestFile, repFile);
	pslFreeList(&pslList);
	safef(lastName, sizeof(lastName), "%s", psl->qName);
	}
    slAddHead(&pslList, psl);
    }
doOneAcc(lastName, pslList, bestFile, repFile);
pslFreeList(&pslList);
lineFileClose(&in);
fclose(bestFile);
fclose(repFile);
if (!quiet)
    printf("Processed %d alignments\n", aliCount);
}

int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 4)
    usage();
minAli = optionFloat("minAli", minAli);
nearTop = optionFloat("nearTop", nearTop);
minCover = optionFloat("minCover", minCover);
minNearTopSize = optionInt("minNearTopSize", minNearTopSize);
ignoreSize = optionExists("ignoreSize");
if (optionExists("sizeMatters"))
    warn("warning: -sizeMatters is deprecated and is now the default");
noIntrons = optionExists("noIntrons");
singleHit = optionExists("singleHit");
noHead = optionExists("nohead");
ignoreNs = optionExists("ignoreNs");
coverQSizeFile = optionVal("coverQSizes", NULL);
pslReps(argv[1], argv[2], argv[3]);
return 0;
}