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arguments
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Renamed NO_HEADER to the more accurate no_cmdline_in_header
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2012-05-24 10:57:08 -04:00 |
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contexts
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Added function to get bases from the current base forward in the window in ReferenceContext
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2012-04-06 16:07:46 -04:00 |
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datasources
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Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each.
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2012-05-21 15:41:56 -04:00 |
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examples
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As promised in the release notes for 1.6, I am removing the old deprecated genotyping framework revolving around the misordering of alleles and have moved the fixed version in its place in preparation for release 1.7 (or 2.0?).
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2012-05-01 16:18:24 -04:00 |
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executive
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Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.
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2012-04-17 14:22:48 -04:00 |
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filters
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Bug fix in BadCigar read filter for index out of bounds exception when used with a bam file that contains unmapped reads.
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2012-05-21 16:46:59 -04:00 |
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io
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Renamed NO_HEADER to the more accurate no_cmdline_in_header
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2012-05-24 10:57:08 -04:00 |
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iterators
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Committing the best of the frantic pre-CSHL experiments: Better algorithm for partioning reads amongst the alleles they support. Require the read's original alignment to actually overlap the variant. QD uses the non-informative reads when calculating D. More HC-specific annotations for potential use in a statistical filtering strategy. Increasing the minimum kmer length in the assembly graphs. Misc minor bug fixes.
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2012-05-10 13:09:03 -04:00 |
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phonehome
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Capture the class of the exception in GATKRunReport
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2012-03-14 12:16:22 -04:00 |
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refdata
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Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each.
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2012-05-21 15:41:56 -04:00 |
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report
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Fixed up the comments in the GATKReportTable code and added some sanity checks to make sure that the user doesn't inconsistently add rows and corresponding IDs to the table.
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2012-05-21 14:16:13 -04:00 |
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resourcemanagement
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First pass of the asynchronous block loader.
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2011-11-18 15:02:59 -05:00 |
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samples
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Added function to get founders IDs in SampleDB
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2012-04-25 12:49:36 -04:00 |
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traversals
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Merging active regions across shard boundries if they are contiguous, have the same active status and don't grow too big.
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2012-05-01 15:51:36 -04:00 |
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walkers
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AD should be UNBOUNDED, actually
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2012-05-24 10:57:05 -04:00 |
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CommandLineExecutable.java
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Old -B syntax is long gone at this point. Safe to remove the warning.
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2012-04-02 22:25:16 -04:00 |
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CommandLineGATK.java
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OutOfMemory exceptions are User Errors
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2012-04-02 22:46:56 -04:00 |
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DownsampleType.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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DownsamplingMethod.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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GenomeAnalysisEngine.java
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Adding engine capability to quantize qualities.
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2012-04-08 21:07:51 -04:00 |
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ReadMetrics.java
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Counts of records failing filters are displayed sorted
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2011-10-06 18:42:26 -07:00 |
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ReadProperties.java
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Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.
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2012-04-02 14:27:36 -04:00 |
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WalkerManager.java
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Removed support for RMD in @Requires and @Allows
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2011-08-03 15:36:55 -04:00 |
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package-info.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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