src/hg/tcga/pBamBam/asBamBam.c 1.5

Index: src/hg/tcga/pBamBam/asBamBam.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/tcga/pBamBam/asBamBam.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/tcga/pBamBam/asBamBam.c	7 Mar 2010 03:26:33 -0000	1.4
+++ src/hg/tcga/pBamBam/asBamBam.c	7 Mar 2010 03:28:00 -0000	1.5
@@ -26,15 +26,15 @@
   "asBamBam - Allele-Specific BamBam.\n"
   "usage:\n"
   "   asBamBam [options] <left.bam> <right.bam>\n"
   "options:\n"
-  "   -position=chrX:1-100 - Position to do analysis. [None]\n" 
+  "   -position=chr1:1-100 - Position to do analysis. [NULL=process all reads]\n" 
   "   -minSupport=INT   - Minimum Support in Germline. [4]\n"
   "   -minQ=INT         - Minimum acceptable base quality. [10]\n"
   "   -minMapQ=INT      - Minimum acceptable mapping quality. [20]\n"
   "   -avgMapQ=INT      - Minimum acceptable average mapping quality. [30]\n"
   "   -minChiSq=INT     - Minimum acceptable chi square of nucleotide freqs. [250]\n"
-  "   -maxISize=INT     - Maximum Insert Size. [10000]\n"
+  "   -maxISize=INT     - Maximum Insert Size. [2000]\n"
   "   -readsPerBin=INT  - Reads per CNV bin [2500]\n"
   "\n"
   );
 }
@@ -58,9 +58,9 @@
 int minSupport  = 4;
 int minQ        = 10;
 int minMapQ     = 20;
 int avgMapQ     = 30;
-int maxISize    = 10000;
+int maxISize    = 2000;
 int minChiSq    = 250;
 int readsPerBin = 2500;
 
 typedef struct {
@@ -1442,9 +1442,9 @@
     minMapQ = optionInt("minMapQ", 20);
 if (optionExists("avgMapQ"))
     avgMapQ = optionInt("avgMapQ", 30);
 if (optionExists("maxISize"))
-    maxISize = optionInt("maxISize", 10000);
+    maxISize = optionInt("maxISize", 2000);
 if (optionExists("minChiSq"))
     minChiSq = optionInt("minChiSq", 250);
 if (optionExists("readsPerBin"))
     readsPerBin = optionInt("readsPerBin", 2500);