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Valentin Ruano-Rubio c5977e5c8f Correct wrong left-alignment of reads in HC bamout 
Story:
-----

  https://www.pivotaltracker.com/story/show/80684230

Changes:
-------

  - Corrected the bug: AlignmentUtils#createReadAlignedToRef was
    not realigning against the reference but the best haplotype for
    the read.

Test:
----

  - Added integration test in HaplotypeCallerIntegrationTest to check
    that the bug has been fixed.
  - Fixed md5s modified by this change; these are cause due to small
    changes in the state of the random-number generator and read vs
    variant site overlapping.
 		2014-11-10 10:09:58 -05:00
..
VectorPairHMM Update pom versions to mark the start of GATK 3.4 development 2014-10-23 22:31:44 -04:00
c After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive. 2014-05-19 17:36:41 -04:00
chainFiles The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -04:00
doc Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
external-example Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00
gatk-engine Catch RuntimeException and add the bad file name to the newly thown exception 2014-11-05 09:14:33 -05:00
gatk-queue Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00
gatk-queue-extensions-generator Split all imports of tools|engine from utils, and all tools from engine. 2014-10-24 20:59:46 +08:00
gatk-queue-extensions-public Disabling tests for Lsf706 specific functionality. 2014-11-04 01:31:18 +08:00
gatk-root Merge pull request #768 from broadinstitute/pd_bcf_failures 2014-10-31 15:30:56 -04:00
gatk-tools-public Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00
gatk-utils Correct wrong left-alignment of reads in HC bamout 2014-11-10 10:09:58 -05:00
gsalib Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Split all imports of tools|engine from utils, and all tools from engine. 2014-10-24 20:59:46 +08:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Revved Picard/htsjdk 2014-10-30 21:16:25 -04:00
src/main Added faster built executable, non-packaged jars. 2014-11-05 00:30:46 +08:00
pom.xml Update pom versions to mark the start of GATK 3.4 development 2014-10-23 22:31:44 -04:00