a1693312d826bef79bda3d13693a80055d43f705
braney
  Tue Aug 4 12:15:39 2015 -0700
left out bigPsl.c in my earlier bigPsl check in.   #14241

diff --git src/hg/lib/bigPsl.c src/hg/lib/bigPsl.c
new file mode 100644
index 0000000..5d01be7
--- /dev/null
+++ src/hg/lib/bigPsl.c
@@ -0,0 +1,336 @@
+/* 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 + 11 - 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]);
+    if (*psl->strand == '-')
+	reverseComplement(*seq, strlen(*seq));
+    }
+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->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;
+    }
+
+return psl;
+}