src/hg/tcga/pBamBam/asBamBam.c 1.12

Index: src/hg/tcga/pBamBam/asBamBam.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/tcga/pBamBam/asBamBam.c,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 4 -r1.11 -r1.12
--- src/hg/tcga/pBamBam/asBamBam.c	1 Jun 2010 21:46:13 -0000	1.11
+++ src/hg/tcga/pBamBam/asBamBam.c	1 Jun 2010 22:04:29 -0000	1.12
@@ -36,8 +36,9 @@
   "   -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. [2000]\n"
   "   -readsPerBin=INT  - Reads per CNV bin [2500]\n"
+  "   -fracGerm=FLOAT   - Fraction of normal contamination [0.0]\n"
   "\n"
   );
 }
 
@@ -69,8 +70,9 @@
 int avgMapQ     = 30;
 int maxISize    = 2000;
 int minChiSq    = 250;
 int readsPerBin = 2500;
+float fracGerm  = 0.0;
 
 typedef struct {
     int minQ;
     int minMapQ;
@@ -1756,8 +1758,12 @@
 
 ap.svStartR = -1;
 ap.svStopR  = -1;
 
+ap.fracGerm = (long double) fracGerm;
+
+initProbTables();
+
 reset_intra();
 reset_inter();
 
 bam_bam_file(inbamL, inbamR, faidx, position, mask, perform_analysis, &ap);
@@ -1790,8 +1796,10 @@
 if (optionExists("minChiSq"))
     minChiSq = optionInt("minChiSq", 250);
 if (optionExists("readsPerBin"))
     readsPerBin = optionInt("readsPerBin", 2500);
+if (optionExists("fracGerm"))
+    fracGerm = optionFloat("fracGerm", 0.0);
 
 char *inbamL = argv[1];
 char *inbamR = argv[2];
 bamBam(inbamL, inbamR, faidx, BAM_DEF_MASK);