1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
9f3b99c11b
Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.
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Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 03:41:07 +00:00
d25a2fe120
Better handling of enums by the command-line argument system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2647 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 21:36:46 +00:00
35a4fcc481
Additional sanity checking: make sure the user can't alter the header / compression level / presorted state of a file to which SAMRecords have already been written.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2562 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:39:41 +00:00
58999a8e9d
Enhance the I/O management system to support custom headers and set the presorted flag
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from the initialize() method (or at any time before the first SAM record is written).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2560 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:21:42 +00:00
e32174fbc4
UnifiedGenotyper now works without -varout or -vf set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2464 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 16:46:24 +00:00
b125571a98
Intermediate check in: transfer responsibility of wrapping the GenotypeWriter around the output stream to the output
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management code. Currently, will not work when neither -varout nor -vf are specified, but should work in all other
cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2463 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 16:11:11 +00:00
aeb34758e6
Adding a validation stringency to the VCF writers (which defaults to STRICT). If set to SILENT, it will not throw an exception for (reasonable) off-spec requests but will instead ignore such requests and silently move on.
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This change allows the pooled calculation model to work correctly with multiple threads. Boys, the Genotyper is now officially parallelized.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2462 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 15:33:53 +00:00
159778416c
In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2435 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 21:42:36 +00:00
0d890e1bf0
Rework Eric's output management code given that the behavior of the UG changes drastically
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depending on its output format. Current implementation is probably a bit overkill-ish and
we can whittle this down to what's absolutely necessary.
Writing VCFs to the 'out' protected printstream may not work at this moment.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2425 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 00:33:43 +00:00
b780ffb34a
Add a getFormat() method to get the output format from the writer. The need for
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this call suggests that I may be thinking about the typing of the GenotypeWriter object the wrong way.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2418 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 01:46:26 +00:00
11cbfcec9c
Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple
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source -> single definition mapping sets.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2417 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 00:39:36 +00:00
9e53c06328
First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2416 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 19:19:23 +00:00
7e0f69dab5
Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2410 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 22:54:56 +00:00
4ea31fd949
Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2406 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 19:16:41 +00:00
4f59bfd513
Updates to the various GenotypeWriters to make them do simple things like write records (plus allow GLFReader to close).
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Adding first pass of stub and storage classes for the GenotypeWriters so that UG can be parallelizable. Not hooked up yet, so UG is unchanged.
The mergeInto() code in the storage class is ugly, but it's all Tribble's fault. We can clean it up later if this whole thing works.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2400 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 07:20:23 +00:00
0c396f04a2
Fix obvious cut/paste error in output stream management code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2313 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:23:13 +00:00
a1e8a532ad
Support for initialize() and onTraversalDone() output from parallelized walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1911 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 20:18:31 +00:00
d844d1c496
SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1807 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 19:16:46 +00:00
da084357db
Fixed minor typo in output message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1806 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 18:56:54 +00:00
70e1aef550
Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 22:23:19 +00:00
856bbd0320
Let Picard specify the default compression level.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1701 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 19:01:48 +00:00
ebfbe56b43
Make sure compression level always gets pushed into SAMFileWriterFactory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1699 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 18:20:26 +00:00
355136928e
Play nice with other jobs in this VM -- don't close stdout / stderr.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1646 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-17 18:55:08 +00:00
01a9b1c63b
Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1634 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-16 08:33:56 +00:00
9f7cf73411
Output stream management fixes. I completely screwed up the output stream management system, but cleverly masked this fact by breaking some other stream management functionality that masked the problem.
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Sigh.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1630 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 21:06:45 +00:00
17758b381c
Properly initialize redirected output streams in case of out and err.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1629 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 19:47:43 +00:00
b69eb208a6
Always create output files, even if no output was written to them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1627 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 17:58:14 +00:00
ccdb4a0313
General-purpose management of output streams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-23 00:56:02 +00:00
hanna
ebanks
alecw
aaron