05fac8583d
Following up Mark's recent commit: hooking up the --maxPositionalMoveAllowed argument into the indel realigner and through to the SAM writer. We now ensure that no read is realigned more than N bases (200 by default, which is nowhere close to realistically possible). If anyone ever sees a warning message about this with the default value then please let me know because I need to see it for myself.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5331 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 04:40:54 +00:00
ce51ffb56e
Oops, old local paths committed on accident.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5200 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 23:35:56 +00:00
29f3ad72f3
SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5199 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:27:05 +00:00
861ee3e37a
Changing testing framework from junit -> testng, for its enhanced configurability.
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Initial test to see how Bamboo will respond. More detailed email to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 21:31:44 +00:00
32d86cf457
Rev the reservoir downsampler to support partitioning through a functor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3232 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:50:26 +00:00
c08936d6f4
Added a reservoir downsampler which can sample elements in an iterator uniformly
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from a stream (see Vitter 1985). Thanks to Eric and Andrey for the pointer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3197 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 20:48:14 +00:00
4014a8a674
A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.
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Thanks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 06:14:15 +00:00
5b1c23a7f2
changes to fix and test the interval based traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:54:15 +00:00
6ee64c7e43
added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:15:56 +00:00
71e3825fa1
First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:18:13 +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
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
eb962fe52a
adding an artificial sam file writer, used to unit test some of the walkers (mainly the PrintReadsWalker)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@956 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 21:47:49 +00:00
109bef6c08
We're no longer in the read-dropping business.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:37:51 +00:00
ebanks
depristo
hanna
aaron