e4ed48ec94fc067795b47dcbda27130a8d007f56
markd
  Mon Jan 18 23:37:48 2016 -0800
fixed problem with bigPslToPsl not computing insert counts.  Base on previous work that was deemed a waste of time

diff --git src/hg/lib/bigPsl.c src/hg/lib/bigPsl.c
index bf99660..4991fba 100644
--- src/hg/lib/bigPsl.c
+++ src/hg/lib/bigPsl.c
@@ -1,337 +1,338 @@
 /* bigPsl.c was originally generated by the autoSql program, which also 
  * generated bigPsl.h and bigPsl.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "bigPsl.h"
 #include "psl.h"
 
 
 
 char *bigPslCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,reserved,blockCount,blockSizes,chromStarts,oChromStart,oChromEnd,oStrand,oChromSize,oChromStarts,oSequence,oCDS,oBlock,match,misMatch,repMatch,nCount";
 
 struct bigPsl *bigPslLoad(char **row)
 /* Load a bigPsl from row fetched with select * from bigPsl
  * from database.  Dispose of this with bigPslFree(). */
 {
 struct bigPsl *ret;
 
 AllocVar(ret);
 ret->blockCount = sqlSigned(row[9]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->reserved = sqlUnsigned(row[8]);
 {
 int sizeOne;
 sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 {
 int sizeOne;
 sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 ret->oChromStart = sqlUnsigned(row[12]);
 ret->oChromEnd = sqlUnsigned(row[13]);
 safecpy(ret->oStrand, sizeof(ret->oStrand), row[14]);
 ret->oChromSize = sqlUnsigned(row[15]);
 {
 int sizeOne;
 sqlSignedDynamicArray(row[16], &ret->oChromStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 ret->oSequence = cloneString(row[17]);
 ret->oCDS = cloneString(row[18]);
 ret->oBlock = sqlUnsigned(row[19]);
 ret->match = sqlUnsigned(row[20]);
 ret->misMatch = sqlUnsigned(row[21]);
 ret->repMatch = sqlUnsigned(row[22]);
 ret->nCount = sqlUnsigned(row[23]);
 return ret;
 }
 
 struct bigPsl *bigPslLoadAll(char *fileName) 
 /* Load all bigPsl from a whitespace-separated file.
  * Dispose of this with bigPslFreeList(). */
 {
 struct bigPsl *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[24];
 
 while (lineFileRow(lf, row))
     {
     el = bigPslLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bigPsl *bigPslLoadAllByChar(char *fileName, char chopper) 
 /* Load all bigPsl from a chopper separated file.
  * Dispose of this with bigPslFreeList(). */
 {
 struct bigPsl *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[24];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = bigPslLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bigPsl *bigPslCommaIn(char **pS, struct bigPsl *ret)
 /* Create a bigPsl out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bigPsl */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->reserved = sqlUnsignedComma(&s);
 ret->blockCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->blockSizes, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->blockSizes[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->chromStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->chromStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->oChromStart = sqlUnsignedComma(&s);
 ret->oChromEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->oStrand, sizeof(ret->oStrand));
 ret->oChromSize = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->oChromStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->oChromStarts[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->oSequence = sqlStringComma(&s);
 ret->oCDS = sqlStringComma(&s);
 ret->oBlock = sqlUnsignedComma(&s);
 ret->match = sqlUnsignedComma(&s);
 ret->misMatch = sqlUnsignedComma(&s);
 ret->repMatch = sqlUnsignedComma(&s);
 ret->nCount = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void bigPslFree(struct bigPsl **pEl)
 /* Free a single dynamically allocated bigPsl such as created
  * with bigPslLoad(). */
 {
 struct bigPsl *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->blockSizes);
 freeMem(el->chromStarts);
 freeMem(el->oChromStarts);
 freeMem(el->oSequence);
 freeMem(el->oCDS);
 freez(pEl);
 }
 
 void bigPslFreeList(struct bigPsl **pList)
 /* Free a list of dynamically allocated bigPsl's */
 {
 struct bigPsl *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bigPslFree(&el);
     }
 *pList = NULL;
 }
 
 void bigPslOutput(struct bigPsl *el, FILE *f, char sep, char lastSep) 
 /* Print out bigPsl.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->reserved);
 fputc(sep,f);
 fprintf(f, "%d", el->blockCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->blockSizes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->chromStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%u", el->oChromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->oChromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->oStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->oChromSize);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%u", el->oChromStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->oSequence);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->oCDS);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->oBlock);
 fputc(sep,f);
 fprintf(f, "%u", el->match);
 fputc(sep,f);
 fprintf(f, "%u", el->misMatch);
 fputc(sep,f);
 fprintf(f, "%u", el->repMatch);
 fputc(sep,f);
 fprintf(f, "%u", el->nCount);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct psl  *pslFromBigPsl( char *chrom, struct bigBedInterval *bb, unsigned chromSize, char **seq, char **cds)
 /* build a psl from a bigPsl */
 {
 char *extra = cloneString(bb->rest);
 int numCols = 12 + 12 - 3;
 char *row[numCols];
 int wordCount = chopByChar(extra, '\t', row, numCols);
 assert(wordCount == numCols);
 
 struct psl *psl;
 int ii;
 int sizeOne;
 AllocVar(psl);
 
 psl->qName = cloneString(row[0]); 
 psl->strand[0] = *row[2];
 if ((cds != NULL) && row[15] != NULL)
     *cds = cloneString(row[15]);
 
 if ((seq != NULL) && row[14] != NULL)
     *seq = cloneString(row[14]);
 psl->match = sqlUnsigned(row[17]);
 psl->misMatch = sqlUnsigned(row[18]);
 psl->repMatch = sqlUnsigned(row[19]);
 psl->nCount = sqlUnsigned(row[20]);
 psl->tName = chrom;
 psl->tStart = bb->start;
 psl->tEnd = bb->end;
 psl->tSize = chromSize;
 psl->blockCount = sqlSigned(row[6]);
 sqlUnsignedDynamicArray(row[7], &psl->blockSizes, &sizeOne);
 assert(sizeOne == psl->blockCount);
 sqlUnsignedDynamicArray(row[8], &psl->tStarts, &sizeOne);
 assert(sizeOne == psl->blockCount);
 psl->qStart = sqlSigned(row[9]); 
 psl->qEnd = sqlSigned(row[10]); 
 psl->strand[1] = *row[11];
 psl->strand[1] = 0;
 psl->qSize = sqlSigned(row[12]); 
 sqlUnsignedDynamicArray(row[13], &psl->qStarts, &sizeOne);
 assert(sizeOne == psl->blockCount);
 for(ii=0; ii < psl->blockCount; ii++)
     {
     psl->tStarts[ii] += psl->tStart;
 //    psl->qStarts[ii] += psl->qStart;
     }
 
+pslComputeInsertCounts(psl);
 return psl;
 }