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Commits on Oct 8, 2014

• Release 1.122

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  gbggrant

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Commits on Oct 7, 2014

• Merge pull request #91 from broadinstitute/nh_update_calc_hs_metrics_for_min_interval_lists

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• Updating the minimum number of times that the BAIT_INTERVALS (in CalculateHsMetrics) and TARGET_INTERVALS (in CollectTargetedMetrics) must be set to one.

  

  Nils Homer

  committed
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Commits on Oct 3, 2014

• Merge pull request #89 from broadinstitute/nh_remove_uncessessary_mark_duplicates_storing_read_name

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• - removing unnecessary storage of a string in the Read Ends in Mark

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  Nils Homer

  committed
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• Merge pull request #84 from broadinstitute/gg_genotype_concordance

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Commits on Oct 2, 2014

• Merge pull request #88 from broadinstitute/yf_move_PFFail_to_public

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  Yossi Farjoun

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• Moved CollectHiSeqPfFailMetrics into picard public

  

  Yossi Farjoun

  committed
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• Picard GenotypeConcordance tool

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  tfenne

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  gbggrant

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Commits on Sep 29, 2014

• Merge pull request #85 from broadinstitute/gg_vcf_to_interval_list

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Commits on Sep 27, 2014

• New Command Line Program to create an interval list from a VCF.

  gbggrant

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Commits on Sep 24, 2014

• Merge pull request #82 from broadinstitute/nh_testdata_links_to_github

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• changing link to IntervalList.java documentation

  

  Nils Homer

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• Merge pull request #78 from broadinstitute/nh_cmd_line_usage_docs_fix

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• Merge pull request #71 from broadinstitute/gg_UpdateVcfDictionary

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• Merge pull request #79 from broadinstitute/bt_mark_duplicates

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Commits on Sep 23, 2014

• Adding a new tool with which to mark duplicates:

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  Nils Homer

  committed
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• New CLP to update the sequence dictionary for one with VCF with that from another.

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  gbggrant

  committed
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• updating how _includes/command-line-usage.html is generated on the docs

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  Nils Homer

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Commits on Sep 22, 2014

• Picard version 1.121

  

  bradtaylor

  committed
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Commits on Sep 19, 2014

• Merge pull request #74 from broadinstitute/nh_htsjdk_version_file_update

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• updating location of HTSJDK's version property file

  

  Nils Homer

  committed
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• Merge pull request #75 from broadinstitute/yf_ped_file_update

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  Yossi Farjoun

  committed
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• - Added a static function to PedFile that allows the creation of a pedFile object from a Map<String,Sex>.

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  Yossi Farjoun

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Commits on Sep 14, 2014

• Merge pull request #70 from broadinstitute/kt_fix_qual_rewrite_for_bams

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• Fix so BAMRecordCodec will recognize when qual array has been changed.

  ktibbett

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Commits on Sep 12, 2014

• Merge pull request #68 from broadinstitute/bt_sort_vcf_enhancement_PFB-981

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  bradtaylor

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• Merge pull request #64 from broadinstitute/nh_really_fix_supplementals

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  nh13

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• Supplemental alignments are now considered when fixing mate information

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  Nils Homer

  committed
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• SortVcf changes to address code review

  

  bradtaylor

  committed
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• Generalized MergeVcfTest and added a unit test specific to SortVCF

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  bradtaylor

  committed
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• Moved SortVCF to public

  

  bradtaylor

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Commits on Sep 11, 2014

• Merge pull request #67 from broadinstitute/kt_revert_sam_use_oq_for_detection

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  ktibbett

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• Use original qualities to detect encoding scheme if they are being restored.

  ktibbett

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Commits on Sep 10, 2014

• Merge pull request #65 from broadinstitute/tf_samtofastq_singleopen

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  Tim Fennell

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