f972963918
GATK-73 updated docs for bqsr args GATK-9 differentiate CountRODs from CountRODsByRef GATK-76 generate GATKDoc for CatVariants GATK-4 made resource arg required GATK-10 added -o, some docs to CountMales; some docs to CountLoci GATK-11 fixed by MC's -o change; straightened out the docs. GATK-77 fixed references to wiki GATK-76 Added Ami's doc block GATK-14 Added note that these annotations can only be used with VariantAnnotator GATK-15 specified required=false for two arguments GATK-23 Added documentation block GATK-33 Added documentation GATK-34 Added documentation GATK-32 Corrected arg name and docstring in DiffObjects GATK-32 Added note to DO doc about reference (required but unused) GATK-29 Added doc block to CountIntervals GATK-31 Added @Output PrintStream to enable -o GATK-35 Touched up docs GATK-36 Touched up docs, specified verbosity is optional GATK-60 Corrected GContent annot module location in gatkdocs GATK-68 touched up docs and arg docstrings GATK-16 Added note of caution about calling RODRequiringAnnotations as a group GATK-61 Added run requirements (num samples, min genotype quality) Tweaked template and generic doc block formatting (h2 to h3 titles) GATK-62 Added a caveat to HR annot Made experimental annotation hidden GATK-75 Added setup info regarding BWA GATK-22 Clarified some argument requirements GATK-48 Clarified -G doc comments GATK-67 Added arg requirement GATK-58 Added annotation and usage docs GSATDG-96 Corrected doc Updated MD5 for DiffObjectsIntegrationTests (only change is link in table title) |
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| scripts/org/broadinstitute/sting | ||
| src/org/broadinstitute/sting/utils/R/gsalib | ||