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Valentin Ruano-Rubio 7acf2eb0e7 Added a more efficient implementation of the KBest haplotype finder code. 
Story:

  https://www.pivotaltracker.com/story/show/66238286

Changes:

  1. Created a new k-best haplotype search implementation in class KBestHaplotypeFinder.
  2. Changed HC code to use the new implementation.
  This seems to fix the original problem without causing significant changes in outputs using some empirical data test cases
  3. Moved haplotype's cigar calculation code from Path to CigarUtils; need that in order to gain independence from Path in some parts of the code.
     In any case that seems like a more natural location for that functionality.
 		2014-03-04 12:22:14 -05:00
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c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
external-example Fixed mvn run for packagetests over external-example. 2014-02-22 01:21:34 +08:00
gatk-framework Added a more efficient implementation of the KBest haplotype finder code. 2014-03-04 12:22:14 -05:00
gatk-package Fixed scope for test-jar depedencies. 2014-02-22 01:21:34 +08:00
gatk-queue-extgen Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
gsalib Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Separate failsafe directories for each of the integration test types [#66515572] 2014-02-27 04:43:39 +08:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Added tests for cleaning up scattered .bai files, and using the log directory. 2014-02-26 02:11:28 +08:00
queue-package Fixed scope for test-jar depedencies. 2014-02-22 01:21:34 +08:00
repo Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
sting-root Attempting to limit gc during Maven tests, using defaults found in JavaCommandLineFunction 2014-03-01 15:24:45 +08:00
sting-utils Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
pom.xml Adding the external example to the build. 2014-02-15 01:26:07 +08:00