src/hg/inc/hapmapSnps.h 1.7
1.7 2009/03/06 23:19:40 angie
HapMap SNPs: Added distinction between expected and observed heterozygosity for filtering. Finally checking in Phase III filtering code in hgTracks/hapmapTrack.c.
Index: src/hg/inc/hapmapSnps.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/hapmapSnps.h,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/inc/hapmapSnps.h 3 Mar 2009 01:07:24 -0000 1.6
+++ src/hg/inc/hapmapSnps.h 6 Mar 2009 23:19:40 -0000 1.7
@@ -74,38 +74,21 @@
#define HAP_TYPE "hapmapSnps_polyType"
#define HAP_MIN_FREQ "hapmapSnps_minorAlleleFreqMinimum"
#define HAP_MAX_FREQ "hapmapSnps_minorAlleleFreqMaximum"
#define HAP_MIN_HET "hapmapSnps_hetMinimum"
-#define HAP_MAX_HET "hapmapSnps_hetMaximum"
+#define HAP_MAX_OBSERVED_HET "hapmapSnps_obsHetMaximum"
+#define HAP_MAX_EXPECTED_HET "hapmapSnps_expHetMaximum"
#define HAP_MONO_PREFIX "hapmapSnps_monomorphic"
#define HAP_ORTHO_PREFIX "hapmapSnps_ortho"
#define HAP_ORTHO_QUAL_PREFIX "hapmapSnps_orthoQual"
-/* OLD -- Keeping these until I can check in the changes to hgTracks/hapmapTrack.c. */
-#define HAP_MONO_CEU "hapmapSnps.monomorphic.ceu"
-#define HAP_MONO_CHB "hapmapSnps.monomorphic.chb"
-#define HAP_MONO_JPT "hapmapSnps.monomorphic.jpt"
-#define HAP_MONO_YRI "hapmapSnps.monomorphic.yri"
-#define HAP_CHIMP "hapmapSnps.chimp"
-#define HAP_CHIMP_QUAL "hapmapSnps.chimpQualScore"
-#define HAP_MACAQUE "hapmapSnps.macaque"
-#define HAP_MACAQUE_QUAL "hapmapSnps.macaqueQualScore"
-#define HAP_POP_MIXED_DEFAULT "no filter"
-#define HAP_POP_COUNT_DEFAULT "no filter"
-#define HAP_TYPE_DEFAULT "no filter"
-#define HAP_MONO_DEFAULT "no filter"
-#define HAP_CHIMP_DEFAULT "no filter"
-#define HAP_CHIMP_QUAL_DEFAULT "0"
-#define HAP_MACAQUE_DEFAULT "no filter"
-#define HAP_MACAQUE_QUAL_DEFAULT "0"
-/* End of old stuff. */
-
#define HAP_FILTER_DEFAULT "no filter"
#define HAP_MIN_FREQ_DEFAULT "0.0"
#define HAP_MAX_FREQ_DEFAULT "0.5"
#define HAP_MIN_HET_DEFAULT "0.0"
-#define HAP_MAX_HET_DEFAULT "0.5"
+#define HAP_MAX_EXPECTED_HET_DEFAULT "0.5"
+#define HAP_MAX_OBSERVED_HET_DEFAULT "1.0"
#define HAP_ORTHO_QUAL_DEFAULT "0"
#define HAP_PHASEII_POPCOUNT 4