75ef8162bbedafcb493516492f28ae951cd8202f
braney
  Tue Nov 20 14:39:59 2018 -0800
fix pslToChain and add tests

diff --git src/hg/pslToChain/pslToChain.c src/hg/pslToChain/pslToChain.c
index 33ba722..70ac3dc 100644
--- src/hg/pslToChain/pslToChain.c
+++ src/hg/pslToChain/pslToChain.c
@@ -4,71 +4,92 @@
  * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "psl.h"
 #include "chain.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "pslToChain - Convert psl records to chain records \n"
   "usage:\n"
   "   pslToChain pslIn chainOut\n"
-  "options:\n"
-  "   -xxx=XXX\n"
+  "Options:\n"
+  "   -ignore   ignore psl records with negative target strand rather than exiting\n"
   );
 }
 
+boolean ignoreError;
+
 static struct optionSpec options[] = {
+   {"ignore", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void pslToChain(char *pslIn, char *chainOut)
 /* pslToChain - Extract multiple psl records. */
 {
 struct lineFile *lf = pslFileOpen(pslIn);
+int chainId = 1;
 int ii;
 FILE *f = mustOpen(chainOut, "w");
 struct psl *psl;
 struct chain chain;
 
 while ((psl = pslNext(lf) ) != NULL)
     {
+    if (psl->strand[1] == '-') 
+        {
+        if (ignoreError)
+            continue;
+        errAbort("PSL record on line %d has '-' for target strand which is not allowed.", lf->lineIx);
+        }
+
     chain.score = pslScore(psl);
-    chain.id = 0;
+    chain.id = chainId++;
     chain.tName = psl->tName;
     chain.tSize = psl->tSize;
     chain.tStart = psl->tStart;
     chain.tEnd = psl->tEnd;
     chain.qName = psl->qName;
     chain.qSize = psl->qSize;
+    chain.qStrand = psl->strand[0];
+
+    if (psl->strand[0] == '-')
+        {
+        chain.qEnd = psl->qSize - psl->qStart;
+        chain.qStart = psl->qSize - psl->qEnd;
+        }
+    else
+        {
         chain.qStart = psl->qStart;
         chain.qEnd = psl->qEnd;
-    chain.qStrand = psl->strand[0];
+        }
     chainWriteHead(&chain,f);
 
     for(ii=0; ii < psl->blockCount; ii++)
 	{
 	fprintf(f, "%d", psl->blockSizes[ii]);
 	if (ii < psl->blockCount - 1)
 	    fprintf(f, "\t%d\t%d", psl->tStarts[ii+1]-(psl->tStarts[ii] + psl->blockSizes[ii]),
 		psl->qStarts[ii+1]-(psl->qStarts[ii] + psl->blockSizes[ii]));
 	fprintf(f,"\n");
 	}
 
 
     pslFree(&psl);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
+ignoreError = optionExists("ignore");
 pslToChain(argv[1], argv[2]);
 return 0;
 }