src/hg/encode/validateFiles/validateFiles.c 1.31

Index: src/hg/encode/validateFiles/validateFiles.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/validateFiles/validateFiles.c,v
retrieving revision 1.30
retrieving revision 1.31
diff -b -B -U 4 -r1.30 -r1.31
--- src/hg/encode/validateFiles/validateFiles.c	9 Dec 2009 19:05:28 -0000	1.30
+++ src/hg/encode/validateFiles/validateFiles.c	9 Dec 2009 19:33:31 -0000	1.31
@@ -64,8 +64,12 @@
   "         fastq     : Fasta with quality scores (see http://maq.sourceforge.net/fastq.shtml)\n"
   "         csfasta   : Colorspace fasta (implies -colorSpace) (see link below)\n"
   "         csqual    : Colorspace quality (see link below)\n"
   "                     (see http://marketing.appliedbiosystems.com/mk/submit/SOLID_KNOWLEDGE_RD?_JS=T&rd=dm)\n"
+  "         SAM       : Sequence Alignment/Map\n"
+  "                     (see http://samtools.sourceforge.net/SAM1.pdf)\n"
+  "         BAM       : Binary Alignment/Map\n"
+  "                     (see http://samtools.sourceforge.net/SAM1.pdf)\n"
   "\n"
   "   -chromDb=db                  Specify DB containing chromInfo table to validate chrom names\n"
   "                                  and sizes\n"
   "   -chromInfo=file.txt          Specify chromInfo file to validate chrom names and sizes\n"
@@ -1024,8 +1028,22 @@
     }
 return errs;
 }
 
+int validateSAM(struct lineFile *lf, char *file)
+{
+int errs = 0;
+
+return errs;
+}
+
+int validateBAM(struct lineFile *lf, char *file)
+{
+int errs = 0;
+
+return errs;
+}
+
 void validateFiles(int (*validate)(struct lineFile *lf, char *file), int numFiles, char *files[])
 /* validateFile - validate format of different track input files. */
 {
 int i;
@@ -1117,8 +1135,10 @@
 hashAdd(funcs, "broadPeak",      &validateBroadPeak);
 hashAdd(funcs, "narrowPeak",     &validateNarrowPeak);
 hashAdd(funcs, "gappedPeak",     &validateGappedPeak);
 hashAdd(funcs, "bedGraph",       &validateBedGraph);
+hashAdd(funcs, "SAM",            &validateSAM);
+hashAdd(funcs, "BAM",            &validateBAM);
 //hashAdd(funcs, "test", &testFunc);
 if (!(func = hashFindVal(funcs, type)))
     errAbort("Cannot validate %s type files\n", type);
 validateFiles(func, argc, argv);