From 8e6093d5a519c6dbc374c4ba0206460463a0ebeb Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 14 Apr 2009 00:45:34 +0000 Subject: [PATCH] remove mom/dad/kid cmd line arguments that were needed for mendelian walker; now we can use generic track binding!! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@389 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/GenomeAnalysisTK.java | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 52273a3d3..aa99d82ee 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -53,12 +53,7 @@ public class GenomeAnalysisTK extends CommandLineProgram { public String DOWNSAMPLE_COVERAGE = null; public String INTERVALS_FILE = null; - // added for mendelian walker. - //TODO: when walkers can ask for their tracks this should be removed! - public String MOTHER_GENOTYPE_FILE = null; - public String FATHER_GENOTYPE_FILE = null; - public String DAUGHTER_GENOTYPE_FILE = null; - + // our walker manager private WalkerManager walkerManager = null; @@ -137,10 +132,6 @@ public class GenomeAnalysisTK extends CommandLineProgram { m_parser.addOptionalArg("numthreads", "nt", "How many threads should be allocated to running this analysis.", "numThreads"); m_parser.addOptionalFlag("enablethreading", "et", "Enable experimental threading support.", "ENABLE_THREADING"); - //TODO: remove when walkers can ask for tracks - m_parser.addOptionalArg("mother", "MOM", "Mother's genotype (SAM pileup)", "MOTHER_GENOTYPE_FILE"); - m_parser.addOptionalArg("father", "DAD", "Father's genotype (SAM pileup)", "FATHER_GENOTYPE_FILE"); - m_parser.addOptionalArg("daughter", "KID", "Daughter's genotype (SAM pileup)", "DAUGHTER_GENOTYPE_FILE"); // --rodBind //m_parser.addOptionalArg("rods", "B", "Bind rod with and to ", "ROD_BINDINGS"); @@ -214,10 +205,6 @@ public class GenomeAnalysisTK extends CommandLineProgram { if ( DBSNP_FILE != null ) bindConvenienceRods("dbSNP", "dbsnp", DBSNP_FILE); if ( HAPMAP_FILE != null ) bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", HAPMAP_FILE); if ( HAPMAP_CHIP_FILE != null ) bindConvenienceRods("hapmap-chip", "GFF", HAPMAP_CHIP_FILE); - //TODO: remove when walkers can ask for tracks - if ( MOTHER_GENOTYPE_FILE != null ) bindConvenienceRods("mother", "SAMPileup", MOTHER_GENOTYPE_FILE); - if ( FATHER_GENOTYPE_FILE != null ) bindConvenienceRods("father", "SAMPileup", FATHER_GENOTYPE_FILE); - if ( DAUGHTER_GENOTYPE_FILE != null ) bindConvenienceRods("daughter", "SAMPileup", DAUGHTER_GENOTYPE_FILE); ReferenceOrderedData.parseBindings(logger, ROD_BINDINGS, rods);