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Commits on Jun 23, 2016

• Fixes for compile failures and warnings and test breaks vs HTSJDK master.

  tfenne

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Commits on Jun 9, 2016

• findbugs:DM_BOOLEAN_CTOR, findbugs:DM_NUMBER_CTOR - Performance - Method invokes inefficient constructor; use static valueOf instead

  

  Mohamed Ezzat

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Commits on May 19, 2016

• squid:S1066 - Collapsible if statements should be merged (#469)

  

  Mohamed Ezzat

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  Yossi Farjoun

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Commits on Apr 15, 2016

• This commit enables MarkDuplicate to process query-sorted input. (#491)

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  Yossi Farjoun

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Commits on Mar 29, 2016

• remove Array program group

  

  Vivek Dasari

  committed
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• Merge pull request #493 from broadinstitute/vd_GTC_to_VCF

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  vivster7

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• add an Array program group

  

  Vivek Dasari

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Commits on Mar 21, 2016

• Adds parser test to check shortName match and removes INTERVALS shortName

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  meganshand

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Commits on Feb 25, 2016

• Revert "Merge pull request #453 from DevFactory/release/Local-variables-should-not-shadow-class-fields-fix-1"

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  Yossi Farjoun

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Commits on Feb 24, 2016

• Merge pull request #456 from DevFactory/release/Append-Character-With-Char-fix-1

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  akiezun

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• Merge pull request #444 from DevFactory/release/Classes-without-public-constructors-should-be-final-fix-1

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  akiezun

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Commits on Feb 22, 2016

• pmd:AppendCharacterWithChar - Append Character With Char

  

  Mohammed Ezzat

  committed
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Commits on Feb 20, 2016

• squid:HiddenFieldCheck - Local variables should not shadow class fields

  

  Mohammed Ezzat

  committed
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Commits on Feb 18, 2016

• Add basic HTML parsing so CLI help is readable

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  Geraldine Van der Auwera

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Commits on Feb 17, 2016

• staging/Collection.isEmpty()-should-be-used-to-test-for-emptiness-fix-1

  

  Mohammed Ezzat

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Commits on Feb 16, 2016

• squid:S2974 - Classes without public constructors should be final

  

  Mohammed Ezzat

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Commits on Jan 7, 2016

• Added some code for comparing sequence data to fingerprints and cross checking it.

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  Eric Banks

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Commits on Nov 23, 2015

• single commit for printOption pull request

  cgirardot

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Commits on Oct 8, 2015

• Modified CommandLineProgram to, when the VALIDATION_STRINGENCY is either LENIENT or SILENT, set the default option on VariantContextWriterBuilder to allow fields that are not defined in the VCFHead…

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  tfenne

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Commits on Sep 8, 2015

• Fix a bug in path handling

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  vdanjean

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Commits on Jun 17, 2015

• Disable escaping html of preamble text in doc generation

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  Geraldine Van der Auwera

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Commits on May 21, 2015

• Print default value for option that is a collection.

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  alecw

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Commits on Mar 27, 2015

• Add support for reading data from Google Genomics implementation of GA4GH API

  iliat

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Commits on Jan 16, 2015

• A recent change to the command line parsing causes problems with scala based CLPs. In cases where the

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  geoffjentry

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Commits on Jan 7, 2015

• Fix overridable option fields.

  jacarey

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Commits on Jan 5, 2015

• print the --list-commands to standard output

  

  Nils Homer

  committed
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Commits on Dec 18, 2014

• adding the --list-commands argument to the main command line, to list

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  Nils Homer

  committed
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• allow colors to be disabled with -Dpicard.cmdline.color_status=false

  

  Nils Homer

  committed
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Commits on Dec 12, 2014

• Merge pull request #124 from broadinstitute/jc_cram_changes

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  jacarey

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Commits on Dec 10, 2014

• Code review changes.

  jacarey

  committed
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Commits on Dec 9, 2014

• Make parseOptionsFile public, with a little more control over behavior.

  alecw

  committed
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• Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes branch of the htsjdk.

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  jacarey

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Commits on Dec 2, 2014

• Various aesthetic tweaks for HTML doc generation.

  mattsooknah

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Commits on Oct 30, 2014

• make getProgramProperty public for things that need to check annotations

  

  Nils Homer

  committed
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Commits on Oct 22, 2014

• This makes a fundamental change to how we run Picard. We now have a

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  nh13

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