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Commits on Jul 6, 2016

• all tests passed

  Evegen55

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Commits on Jul 4, 2016

• fixed concurrency

  Evegen55

  committed
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Commits on Jul 1, 2016

• threads' work analysis

  Evegen55

  committed
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• clear

  Evegen55

  committed
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• second attempt to make a concurrent, succesfull attempt with 1 child thread

  Evegen55

  committed
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• first attempt to make a concurrent, really finished

  Evegen55

  committed
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• first attempt to make a concurrent, finished

  Evegen55

  committed
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Commits on Jun 30, 2016

• first attempt to make a concurrent

  Evegen55

  committed
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• two test have been written for:

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  Evegen55

  committed
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Commits on Jun 29, 2016

• test changes

  Evegen55

  committed
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Commits on Jun 24, 2016

• Merge pull request #573 from broadinstitute/vdauwera-update-README

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  Geraldine Van der Auwera

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  ed61a2f

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• Merge pull request #521 from broadinstitute/dek_docs6

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  Geraldine Van der Auwera

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Commits on Jun 23, 2016

• Improved documentation for multiple tools including

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  dekling

  committed
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• updating version numbers

  lbergelson

  committed
  2c37098

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• Merge pull request #566 from tfenne/tf_fix_htsjdk_master_breaks

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  lbergelson

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

  tfenne

  committed
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Commits on Jun 22, 2016

• Add note on HTSJDK version expectations to README

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  Geraldine Van der Auwera

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  849b283

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• Merge pull request #544 from nh13/nh_per_target_read_counts

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  nh13

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• Output the read count per target.

  nh13

  committed
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Commits on Jun 21, 2016

• Fixing bug in GatherVcfs. (#570)

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  nh13

  authored and

  Yossi Farjoun

  committed
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• Merge pull request #540 from nh13/nh_mergevcfs_clear_options

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  tfenne

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  32db128

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Commits on Jun 14, 2016

• Merge pull request #559 from broadinstitute/kt_fix_revert_sam_for_single_end

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  ktibbett

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Commits on Jun 13, 2016

• Modify RevertSam to set the mate unmapped flag properly for single-end data.

  ktibbett

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Commits on Jun 12, 2016

• Merge pull request #561 from broadinstitute/revert-560-lh_tag_representative_reads

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  lhogstrom

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• Revert "Tag reads in duplicate sets with the representative read and the duplicate set size"

  lhogstrom

  authored
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• Merge pull request #560 from broadinstitute/lh_tag_representative_reads

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  lhogstrom

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• Optional flag added to MarkDuplicates. If true, each record that is part of a duplicate set is tagged with the representative read that is chosen by MarkDuplicates. This is accomplished with the Re…

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  lhogstrom

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Commits on Jun 10, 2016

• Merge pull request #558 from DevFactory/release/maps-with-keys-that-are-enum-values-should-be-replaced-with-enumMap-fix-1

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  ktibbett

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• - fixed TN/NT bug in check fingerprints. (#534)

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  Yossi Farjoun

  authored
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• squid:S1640 - Maps with keys that are enum values should be replaced with

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  Mohamed Ezzat

  committed
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• Merge pull request #557 from DevFactory/release/performance-method-invokes-inefficient-use-valueOf()-instead-fix-1

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  akiezun

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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

  committed
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Commits on Jun 7, 2016

• sprucing-up ScatterIntervalsByNsTest (#543)

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  Yossi Farjoun

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Commits on Jun 3, 2016

• Adding website files for release: 2.4.1-7-gc222883-SNAPSHOT

  jacarey

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Commits on May 31, 2016

• Merge pull request #551 from broadinstitute/dr_fix_sbt_testng_plugin_resolution

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  droazen

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