8a725b6c93
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 23:27:55 +00:00
a7ba88e649
Rework the way the MicroScheduler handles locus shards to handle intervals that span shards
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with less memory consumption.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 18:40:31 +00:00
790d2a7776
adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 15:56:44 +00:00
199b43fcf2
Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a
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simplification of some of the locus traversal code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 00:16:50 +00:00
c3c001e02e
cleanup of the traversal output code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2026 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 06:18:10 +00:00
2ed423ed56
print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2006 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 05:57:01 +00:00
21d1eba502
Cleaned division of responsibilities between arguments to map function. Reference has been changed
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from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:01:37 +00:00
d86717db93
Refactoring of the traversal engine base class, I removed a lot of old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 21:57:00 +00:00
63b5c12cbd
Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:13:22 +00:00
195b4ea7b4
a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 17:46:06 +00:00
ec2f015447
fixed a bunch of comments and license headers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@964 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:10:46 +00:00
36c98b9d6c
added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 01:52:25 +00:00
depristo
hanna
aaron