7bd3ab2b92d48520bf463fd43eeda13318dbe7cb
braney
  Wed Aug 3 12:13:27 2016 -0700
make the doc and AS file for bigPsl a little more explicit about the
file contents

diff --git src/hg/lib/bigPsl.c src/hg/lib/bigPsl.c
index 21df363..f244a1f 100644
--- src/hg/lib/bigPsl.c
+++ src/hg/lib/bigPsl.c
@@ -1,29 +1,29 @@
 /* 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";
+char *bigPslCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,reserved,blockCount,blockSizes,chromStarts,oChromStart,oChromEnd,oStrand,oChromSize,oChromStarts,oSequence,oCDS,chromSize,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]);
@@ -134,31 +134,31 @@
     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);
+    ret->oChromStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->oSequence = sqlStringComma(&s);
 ret->oCDS = sqlStringComma(&s);
 ret->chromSize = sqlUnsignedComma(&s);
 ret->match = sqlUnsignedComma(&s);
 ret->misMatch = sqlUnsignedComma(&s);
 ret->repMatch = sqlUnsignedComma(&s);
 ret->nCount = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
@@ -246,31 +246,31 @@
 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]);
+    fprintf(f, "%d", 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->chromSize);
 fputc(sep,f);