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Commits on Jun 23, 2016

• Improved documentation for multiple tools including

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  dekling

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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 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 May 9, 2016

• Allow RevertSam to output by read group. Support CRAM as output format.

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  David Shiga

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• Allow RevertSam to optionally output by read group. When run with OUTPUT_BY_READGROUP=true, multiple output bams will be created, each containing the reads for a single read group. Support outputti…

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  Dave Shiga

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Commits on May 4, 2016

• fixed number of bases in output (missing a + sign) (#532)

  

  Yossi Farjoun

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Commits on Apr 2, 2016

• Adjusted links and language for CollectRnaSeqMetrics, BaitDesigner, and CollectHsMetrics

  

  dekling

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  Geraldine Van der Auwera

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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 #455 from DevFactory/release/Array-designators-should-be-on-the-type,-not-the-variable-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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Commits on Feb 23, 2016

• squid:S1197 - Array designators [] should be on the type, not the variable

  

  Mohammed Ezzat

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Commits on Feb 20, 2016

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

  

  Mohammed Ezzat

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Commits on Feb 19, 2016

• Only load the overlapping dbSNP sites when using target intervals in

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  nh13

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  tfenne

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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 21, 2016

• Simple CLP for safely converting from IntervalList to BED.

  tfenne

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Commits on Jan 13, 2016

• About to rebase to try eliminating test fails

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  davidbenjamin

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  kbergin

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Commits on Jan 11, 2016

• Merge pull request #386 from broadinstitute/tf_bed_to_il_no_merge

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  tfenne

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• Change BedToIntervalList to be non-destructive by default.

  tfenne

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Commits on Jan 10, 2016

• Allows CollectVariantCallingMetrics to collect metrics over a single sample GVCF.

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  yfarjoun

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Commits on Jan 7, 2016

• Package-wide documentation improvements

  

  Geraldine Van der Auwera

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Commits on Nov 21, 2015

• This modification to IlluminaBasecallsTo* and friends allows the inclusion of M operators in the ReadStructure string. The M operator stands for MolecularIndex and is supposed to identify the origi…

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  yfarjoun

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Commits on Sep 24, 2015

• Changed shorts to ints and needed to add a min function that returns ints to Math Util.

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  kbergin

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Commits on Aug 31, 2015

• refactoring out common code from CollectWgsMetricsFromQuerySorted for testing and reuse

  kcibul

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Commits on Aug 5, 2015

• added a utility function to get the log of a list of doubles.

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  Yossi Farjoun

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Commits on Jul 30, 2015

• Fixed bug that caused BedToIntervalList to flip strand of all features with a strand field. Also fixed the test case so that it correctly tests that the strand doesn't flip!

  tfenne

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Commits on Jul 24, 2015

• Update RExecutor.java

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  golharam

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Commits on Jul 23, 2015

• Modify BedToIntervalList to accept other dictionary files

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  abaumann

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Commits on Jul 16, 2015

• the output of scattering intervals should be .interval_list

  

  Nils Homer

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• - fixed a small bug in IntervalListTool where in some cases bases were not accounted for in the total count (this can lead to non-uniform intervalLists in the scatter)

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  yfarjoun

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Commits on Jul 12, 2015

• Added the normalized minimum coverage over a target to the per-target

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  Yossi Farjoun

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Commits on Jun 10, 2015

• Minor change to BedToIntervalList to make sorting and uniquing optional vs. the prior behaviour of always sorting and uniquing the intervals.

  tfenne

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Commits on May 7, 2015

• Change to IntervalListTools to use the new padded() methods in IntervalList.

  tfenne

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Commits on Apr 15, 2015

• Adding a tool that collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file.

  

  Nils Homer

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Commits on Apr 3, 2015

• Add a new method for scattering intervals whereby we try to estimate the

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  Nils Homer

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