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Commits on Nov 25, 2015

• Update pom versions for the 3.5 release

  

  Geraldine Van der Auwera

  committed
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• Merge remote-tracking branch 'unstable/master'

  

  Geraldine Van der Auwera

  committed
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• Merge pull request #1236 from broadinstitute/gvda_prep_M2_release_1201

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  Geraldine Van der Auwera

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Commits on Nov 24, 2015

• Prep MuTect2 and ContEst for release

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  Geraldine Van der Auwera

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• Merge pull request #1243 from broadinstitute/gvda_rodwalkers_dont_downsample_1179

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  Geraldine Van der Auwera

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Commits on Nov 23, 2015

• Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings

  

  Geraldine Van der Auwera

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• Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest

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  fleharty

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Commits on Nov 22, 2015

• Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes_1237

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  Geraldine Van der Auwera

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• Merge pull request #1241 from broadinstitute/gvda_undeprecate_FindCoveredIntervals_1240

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  Geraldine Van der Auwera

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• Yet more doc improvements prior to 3.5 release

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  Geraldine Van der Auwera

  committed
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• Restore FindCoveredIntervals + add docs

  

  Geraldine Van der Auwera

  committed
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• Merge pull request #1233 from broadinstitute/rhl_fix_example_bcf_dict

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  ronlevine

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• Make the header sequence dictionary match reference

  ronlevine

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Commits on Nov 21, 2015

• Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192

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  Geraldine Van der Auwera

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• Merge pull request #1209 from broadinstitute/gvda_yet_more_doc_fixes_1195

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  Geraldine Van der Auwera

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• Deprecate tools that were outdated or redundant

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  Geraldine Van der Auwera

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• Assorted documentation fixes, enhancements and reorganization.

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  meganshand

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  Geraldine Van der Auwera

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• Merge pull request #1230 from broadinstitute/rhl_htsjdk_picard_1.141

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  ronlevine

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Commits on Nov 20, 2015

• Move htsjdk & picard to version 1.141

  ronlevine

  committed
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• Merge pull request #1223 from broadinstitute/rhl_dict_check

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  ronlevine

  committed
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• Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1

  fleharty

  committed
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• Validate VCF with sequence dictionary

  ronlevine

  committed
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Commits on Nov 18, 2015

• Merge pull request #1222 from broadinstitute/yf_percent_informative_read

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  Yossi Farjoun

  committed
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• adding fraction informative reads annotation.

  yfarjoun

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Commits on Nov 17, 2015

• Merge pull request #1219 from broadinstitute/dr_move_GatherBqsrReports_to_protected

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  Eric Banks

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Commits on Nov 10, 2015

• Move GatherBqsrReports from private to protected

  droazen

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• Merge pull request #1198 from broadinstitute/ldg_moreASannotations

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  ldgauthier

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Commits on Nov 9, 2015

• More allele-specific annotations: AS_QD and AS_InbreedingCoeff

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  ldgauthier

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Commits on Nov 8, 2015

• Merge pull request #1193 from broadinstitute/vrr_general_independent_af_calculator

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  Valentin Ruano Rubio

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Commits on Nov 7, 2015

• Added the AF indepdent calculator for any ploidy but seems that is not doing a good job for haploid

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  vruano

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Commits on Nov 6, 2015

• Merge pull request #1207 from broadinstitute/mf_SV_bugfix

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  fleharty

  committed
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• Resolves issue #1061 to use testid1 rather than testid in two integrationtests.

  fleharty

  committed
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Commits on Nov 5, 2015

• Merge pull request #1206 from broadinstitute/eb_suppress_alt_allele_warnings

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  Eric Banks

  committed
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• Suppress emission of the scary warning message from genotyping to no more than once in

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  Eric Banks

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• Merge pull request #1204 from broadinstitute/ms_fix_SelectVariants

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  ldgauthier

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