src/hg/pslMap/pslMap.c 1.17

Index: src/hg/pslMap/pslMap.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/pslMap/pslMap.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -b -B -U 4 -r1.16 -r1.17
--- src/hg/pslMap/pslMap.c	27 Jul 2007 05:26:19 -0000	1.16
+++ src/hg/pslMap/pslMap.c	10 Jul 2009 18:11:56 -0000	1.17
@@ -20,8 +20,9 @@
     {"chainMapFile", OPTION_BOOLEAN},
     {"swapMap", OPTION_BOOLEAN},
     {"swapIn", OPTION_BOOLEAN},
     {"mapInfo", OPTION_STRING},
+    {"mappingPsls", OPTION_STRING},
     {"simplifyMappingIds", OPTION_BOOLEAN},
     {NULL, 0}
 };
 
@@ -32,8 +33,9 @@
 static boolean swapMap = FALSE;
 static boolean swapIn = FALSE;
 static boolean simplifyMappingIds = FALSE;
 static char* mapInfoFile = NULL;
+static char* mappingPslFile = NULL;
 
 static char *mapInfoHdr =
     "#srcQName\t" "srcQStart\t" "srcQEnd\t" "srcQSize\t"
     "srcTName\t" "srcTStart\t" "srcTEnd\t"
@@ -211,9 +213,9 @@
 freeMem(oldQName);
 }
 
 static void mapPslPair(struct psl *inPsl, struct mapAln *mapAln,
-                       FILE* outPslFh, FILE *mapInfoFh)
+                       FILE* outPslFh, FILE *mapInfoFh, FILE *mappingPslFh)
 /* map one pair of query and target PSL */
 {
 struct psl* mappedPsl;
 if (inPsl->tSize != mapAln->psl->qSize)
@@ -229,22 +231,24 @@
         addQNameSuffix(mappedPsl);
     pslTabOut(mappedPsl, outPslFh);
     if (mapInfoFh != NULL)
         writeMapInfo(mapInfoFh, inPsl, mapAln, mappedPsl);
+    if (mappingPslFh != NULL)
+        pslTabOut(mapAln->psl, mappingPslFh);
     }
 pslFree(&mappedPsl);
 }
 
 static void mapQueryPsl(struct psl* inPsl, struct chromBins *mapAlns,
-                        FILE* outPslFh, FILE *mapInfoFh)
+                        FILE* outPslFh, FILE *mapInfoFh, FILE *mappingPslFh)
 /* map a query psl to all targets  */
 {
 static struct dyString *idBuf = NULL;
 struct binElement *overMapAlns
     = chromBinsFind(mapAlns, getMappingId(inPsl->tName, &idBuf), inPsl->tStart, inPsl->tEnd);
 struct binElement *overMapAln;
 for (overMapAln = overMapAlns; overMapAln != NULL; overMapAln = overMapAln->next)
-    mapPslPair(inPsl, (struct mapAln *)overMapAln->val, outPslFh, mapInfoFh);
+    mapPslPair(inPsl, (struct mapAln *)overMapAln->val, outPslFh, mapInfoFh, mappingPslFh);
 slFreeList(&overMapAlns);
 }
 
 static void pslMap(char* inPslFile, char *mapFile, char *outPslFile)
@@ -252,9 +256,9 @@
 {
 struct chromBins *mapAlns;
 struct psl* inPsl;
 struct lineFile* inPslLf = pslFileOpen(inPslFile);
-FILE *outPslFh, *mapInfoFh = NULL;
+FILE *outPslFh, *mapInfoFh = NULL, *mappingPslFh = NULL;
 
 if (chainMapFile)
     mapAlns = loadMapChains(mapFile);
 else
@@ -265,15 +269,18 @@
     {
     mapInfoFh = mustOpen(mapInfoFile, "w");
     fputs(mapInfoHdr, mapInfoFh);
     }
+if (mappingPslFile != NULL)
+    mappingPslFh = mustOpen(mappingPslFile, "w");
 while ((inPsl = pslNext(inPslLf)) != NULL)
     {
     if (swapIn)
         pslSwap(inPsl, FALSE);
-    mapQueryPsl(inPsl, mapAlns, outPslFh, mapInfoFh);
+    mapQueryPsl(inPsl, mapAlns, outPslFh, mapInfoFh, mappingPslFh);
     pslFree(&inPsl);
     }
+carefulClose(&mappingPslFh);
 carefulClose(&mapInfoFh);
 carefulClose(&outPslFh);
 lineFileClose(&inPslLf);
 }
@@ -291,8 +298,9 @@
 swapMap = optionExists("swapMap");
 swapIn = optionExists("swapIn");
 simplifyMappingIds = optionExists("simplifyMappingIds");
 mapInfoFile = optionVal("mapInfo", NULL);
+mappingPslFile = optionVal("mappingPsls", NULL);
 pslMap(argv[1], argv[2], argv[3]);
 
 return 0;
 }