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arguments
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Removing used --enable_overlap_filters argument; Eric assures me this won't break the currently broken tests
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2010-08-09 22:27:13 +00:00 |
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contexts
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fix for a problem in readNextRecord() of BFS, where we'd go looking for the next record far into in the next contig because (f.getEnd() >= start) was never true once we cycled to a new conitg. Added a check for contig identity. Also, removed duplicate HW calculation classes in the GATK and Tribble.
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2010-08-11 17:01:38 +00:00 |
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datasources
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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examples
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Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes
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2010-02-05 21:47:54 +00:00 |
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executive
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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filters
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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io
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Unit, integration, and performance tests are all busted, so this is a good time to make a big commit...
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2010-08-10 04:18:29 +00:00 |
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iterators
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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refdata
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moving tests over from the GATK to Tribble, and added a speed-up to the readNextRecord() that Mark suggested. Also removed the contained flag from the queries to Tribble in the GATK.
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2010-08-10 17:54:59 +00:00 |
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traversals
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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walkers
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Shame on us. FlagStat used ints instead of longs, so we ended up getting negative read counts
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2010-08-13 03:00:57 +00:00 |
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CommandLineExecutable.java
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merging now very close to working. Bug todo in writer and vcf infrastructure. Can almost create merged snp and indel files
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2010-07-02 20:09:25 +00:00 |
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CommandLineGATK.java
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Changed logging level to default at INFO instead of WARN.
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2010-08-09 16:42:48 +00:00 |
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DownsampleType.java
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We're unable to make the naive deduper more worldly, so we're killing it instead.
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2010-06-18 13:54:27 +00:00 |
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DownsamplingMethod.java
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We're unable to make the naive deduper more worldly, so we're killing it instead.
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2010-06-18 13:54:27 +00:00 |
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GATKErrorReport.java
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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GenomeAnalysisEngine.java
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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ReadMetrics.java
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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ReadProperties.java
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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WalkerManager.java
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Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).
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2010-08-11 21:58:26 +00:00 |
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package-info.java
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
f874e548aa