src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c 1.28
1.28 2009/12/01 06:53:14 baertsch
remove commented code
Index: src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c,v
retrieving revision 1.27
retrieving revision 1.28
diff -b -B -U 4 -r1.27 -r1.28
--- src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c 1 Dec 2009 06:46:18 -0000 1.27
+++ src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c 1 Dec 2009 06:53:14 -0000 1.28
@@ -18,9 +18,8 @@
#include "genePredReader.h"
#include "dystring.h"
#include "pseudoGeneLink.h"
#include "verbose.h"
-//#include "twoBit.h"
#include "nibTwo.h"
#include "bed.h"
#include "snp125.h"
#include "pipeline.h"
@@ -60,9 +59,8 @@
char *scoreOut = NULL;
char *snpFile = NULL; /* snp tab file (browser format)*/
int histogram[256][256]; /* histogram of counts for suff statistics, index is a,c,g,t,-,. */
float histoNorm[256][256]; /* normalized histogram for suff statistics, index is a,c,g,t,-,. */
-//static int lociMap[MAXLOCI];
/* command line */
static struct optionSpec optionSpecs[] = {
{"species1", OPTION_STRING},
@@ -274,24 +272,8 @@
{
struct loci *loci = NULL;
bool found = FALSE;
-//for (loci = *lociList ; loci != NULL ; loci = loci->next)
-// {
-// if (sameString(psl->tName, loci->chrom) &&
-// psl->tStart == loci->chromStart && psl->tEnd == loci->chromEnd)
-// errAbort("loci already added %s:%d-%d loci %d-%d\n",
-// psl->tName, psl->tStart, psl->tEnd, loci->chromStart, loci->chromEnd);
-// if (sameString(psl->tName, loci->chrom) &&
-// positiveRangeIntersection(psl->tStart, psl->tEnd, loci->chromStart, loci->chromEnd))
-// {
-// loci->chromStart = min(loci->chromStart, psl->tStart);
-// loci->chromEnd = max(loci->chromEnd, psl->tEnd);
-// verbose(4, "already added %s:%d-%d loci %d-%d\n",
-// psl->tName, psl->tStart, psl->tEnd, loci->chromStart, loci->chromEnd);
-// found = TRUE;
-// }
-// }
if (!found)
{
AllocVar(loci);
loci->chrom = cloneString(psl->tName);
@@ -329,9 +311,8 @@
{
struct loci *loci = NULL;
for (loci = lociList ; loci != NULL ; loci = loci->next)
if (sameString(chrom, loci->chrom) && chromStart == loci->chromStart )
- //&& positiveRangeIntersection(chromStart, chromStart+1, loci->chromStart, loci->chromEnd))
return loci->index;
return -1;
}
@@ -646,15 +627,8 @@
mrnaMisMatch->strands[i] = mme->strand;
mrnaMisMatch->loci[i] = mme->loci;
assert(mrnaMisMatch->loci[i] != NOVALUE);
prevLoc = mme->mrnaLoc;
- /*
- if (slCount(mm) == seqCount)
- if (slCount(mm) < seqCount)
- {
- verbose(5,"1\n");
- }
- */
}
slReverse(&misMatchList);
return misMatchList;
}
@@ -692,23 +666,17 @@
int indel = 0; /* count of gaps in mrna alignment */
int maxScore = -99999; /* max scoring alignment for this mrna */
int nextBestScore = -99999; /* 2nd best scoring alignment for this mrna */
int maxHits = 0; /* number of alignments with max score */
-//int maxIndex = -1; /* index in loci list of best aligment */
int qNameCount = 0; /* count of filtered psls for this qName */
-//int i = 0;
-//int prevLoc = misMatchList->mrnaLoc;
if (misMatchList == NULL)
return FALSE;
-//AllocArray(matchCount,seqCount);
AllocArray(missCount,seqCount);
AllocArray(goodCount,seqCount);
AllocArray(gapCount,seqCount);
AllocArray(neither,seqCount);
AllocArray(snpCount,seqCount);
mrnaMm = tabulateMisMatches(misMatchList, seqCount, lociList);
-//if (sameString(name, "AB032253") || sameString(name, "AB001451"))
-// printf("seq count = %d\n",seqCount);
for (mrnaMisMatch = mrnaMm ; mrnaMisMatch != NULL ;
mrnaMisMatch = mrnaMisMatch->next)
{
int i = 0;
@@ -805,9 +773,8 @@
/* calculate scores for each loci*/
for (l = lociList ; l != NULL; l=l->next)
{
int z = l->index;
- //bool posOk = getLociPosition(lociList, l->index, &chrom, &chromStart, &chromEnd, &psl);
psl = l->psl;
int notAligned = psl->qSize-goodCount[z]-missCount[z]-indel-(psl->match);
if (notAligned < 0) notAligned = 0;
int score = goodCount[z]-missCount[z] - notAligned/notAlignPenalty;
@@ -828,9 +795,8 @@
int score = l->score;
if (maxScore == score)
{
maxHits ++;
- // nextBestScore = score;
verbose(3,"%s score %d == maxScore %d next %d maxHits %d\n",
name, score, maxScore, nextBestScore, maxHits);
}
else
@@ -965,11 +931,8 @@
}
int getHistogram(char a, char b)
{
-//if (a == 'N')
-// return(histogram[(unsigned int)'a'][(unsigned int)b] + histogram[(unsigned int)'c'][(unsigned int)b] + histogram[(unsigned int)'g'][(unsigned int)b] + histogram[(unsigned int)'t'][(unsigned int)b] );
-//else
return(histogram[(unsigned int)a][(unsigned int)b]);
}
float getHistoNorm(char a, char b)
@@ -1084,25 +1047,8 @@
// }
freeDnaSeq(&tSeq);
freeDnaSeq(&qSeq);
}
-/*
-for (i = 0 ; i < 256 ; i++)
- for (j = 0 ; j < 256 ; j++)
- sum += histogram[i][j] ;
- fprintf(outFile, "%5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %5.4f %s ",
- getHistogram('a','a')/sum, getHistogram('a','c')/sum, getHistogram('a','g')/sum, getHistogram('a','t')/sum,
- getHistogram('c','a')/sum, getHistogram('c','c')/sum, getHistogram('c','g')/sum, getHistogram('c','t')/sum,
- getHistogram('g','a')/sum, getHistogram('g','c')/sum, getHistogram('g','g')/sum, getHistogram('g','t')/sum,
- getHistogram('t','a')/sum, getHistogram('t','c')/sum, getHistogram('t','g')/sum, getHistogram('t','t')/sum , psl->qName
- );
- fprintf(outFile,"Transitions %5.4f Transversions %5.4f Matches %5.4f\n",
- (getHistogram('a','g')+ getHistogram('g','a')+ getHistogram('c','t')+ getHistogram('t','c'))/sum,
- (getHistogram('a','c')+ getHistogram('a','t')+ getHistogram('c','a')+ getHistogram('c','g')+
- getHistogram('g','c')+ getHistogram('g','t')+ getHistogram('t','a')+ getHistogram('t','g'))/sum,
- (getHistogram('a','a')+ getHistogram('c','c')+ getHistogram('g','g')+ getHistogram('t','t'))/sum
- );
- */
}
void addOtherAlignments( struct alignment *alignList, struct hash *speciesHash, char *name, char *nibDir, char *mrnaPath)
{
@@ -1133,9 +1079,8 @@
struct psl *psl = align->psl;
struct nibInfo *tNib = nibInfoFromCache(nibHash, align->nibDir, psl->tName);
int tStart = psl->tStart;
int tEnd = psl->tEnd;
- //int misMatchCount = 0;
char genomeStrand = psl->strand[1] == '-' ? '-' : '+';
int index = getLoci(lociList, psl->tName, psl->tStart);
@@ -1195,30 +1140,16 @@
verbose(5,"GOOD\n");
else
verbose(5,"MISMATCH\n");
}
- /* else if (i < 0)
- {
- mm->chrom = cloneString(psl->tName);
- mm->chromStart = -1;
- mm->genomeBase = '-';
- mm->strand = genomeStrand;
- verbose(2, "negative index %s %s mrnaLoc %d qs %d \n",psl->qName, psl->tName, mm->mrnaLoc , qs);
- }*/
/* if we are outside the block, assume an indel */
else if (mm->mrnaLoc >= qs && mm->mrnaLoc < qe)
{
mm->genomeBase = '-';
verbose(5," fM() INDEL %s t %s:%d mrnaLoc %d i %d not in %d-%d %s loci %d BLK %d\n",
psl->qName, psl->tName,
psl->tStart, mm->mrnaLoc, i, qs, qe , psl->strand, mm->loci, blockIx);
}
-// else
-// {
-// verbose(5," fM() nop %s chr %s t %s:%d mrnaLoc %d i %d not in %d-%d %s loci %d <> %d BLK %d\n",
-// psl->qName, mm->chrom, psl->tName,
-// psl->tStart, mm->mrnaLoc, i, qs, qe, psl->strand, mm->loci, index, blockIx);
-// }
}
}
/*
snpList = getSnpList(psl->tName, ts, te, genomeStrand) ;
@@ -1250,10 +1181,8 @@
int transitionCount = 0;
int transversionCount = 0;
char genomeStrand = psl->strand[1] == '-' ? '-' : '+';
int matchCount = 0;
-//if (genomeStrand == '-')
-// reverseIntRange(&tStart, &tEnd, psl->tSize);
for (blockIx=0; blockIx < psl->blockCount; ++blockIx)
/* for each alignment block get sequence for both strands */
{
struct snp125 *snp = NULL, *snpList = NULL;
@@ -1568,9 +1497,8 @@
verbosity = optionInt("verbose", verbosity);
verboseSetLogFile("stdout");
verboseSetLevel(verbosity);
ss = axtScoreSchemeDefault();
-//mrnaHash = readPslToBinKeeper(argv[2], argv[1]);
twoBitFile = twoBitOpen(argv[3]);
outFile = fopen(argv[5],"w");
initSS();