0aba688e6f
Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@609 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:40:41 +00:00
98716138e9
Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions.
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Made fields of command-line argument system non-public by default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@606 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 19:38:05 +00:00
f5eae98af2
Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@605 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:40:55 +00:00
ef211f96b1
Remove old Apache CLI-based arg system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@604 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:37:51 +00:00
521aa40baa
Bring new command-line argument parsing system live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@603 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:16:11 +00:00
4ac9e72739
Migrate default and GATK arguments over to new attribute system in preparation for conversion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@600 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:57:48 +00:00
b0cdba8bb3
Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:43:40 +00:00
f5880109a7
Added TraverseReads test, some bug fixes discovered in the traversal test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@594 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 20:36:00 +00:00
daa2163ee8
Made the MergingSamIterator2 peekable. This iterator is being a ducktaped together swiss army knife, the iterators could use a redo soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@593 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 19:15:07 +00:00
09b0b6b57d
Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@592 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 18:17:07 +00:00
6e38966349
Rename some key classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@587 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 22:01:04 +00:00
5bdf653919
Cleanup: prepare for better output handling.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@586 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:40:46 +00:00
9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
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-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 19:34:09 +00:00
84dae06d5a
Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@576 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:16:21 +00:00
ff420f5f6f
Enabled iterator() function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@575 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:15:14 +00:00
63403d32cd
Changes to the interface to the simple data source rippled out to a bunch of files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@572 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:35:56 +00:00
7f173af2ea
Encapsulate output tracking a bit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@570 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 15:12:13 +00:00
ba9a0b5da8
Break out some of the weird inner classes out of the HierachicalMicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@566 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 21:07:07 +00:00
95d10ba314
Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@565 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 20:26:16 +00:00
7de5da7065
Start getting the cleaner working in Walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@561 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 14:59:53 +00:00
6ecc43f385
Provide a default logger, some config settings, and some doc updates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@557 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 02:06:05 +00:00
b836761104
removed the test cases from the bottom of this file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@556 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 21:50:22 +00:00
d4de68e260
added changes for the readsTraversal to accomidate design changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@553 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 19:49:58 +00:00
b6874f30cb
Added changes to bounded read iterator, it now explicitly takes a MSRI2 instead of the interfaces ClosableIterator<SAMRecord>. It would be good to fix this in the future with an interface that lets you get the (possibly merged) header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@552 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 17:57:54 +00:00
395aaf48b0
Added the new by reads traversal, still needs to be sewn into the micromanager code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@551 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 17:55:08 +00:00
a343f3eab7
Fixed bug where we weren't setting the reads group correctly. Also added code to set the printMetrics field of the singleSampleGenotyper from the Pool caller, it was null excepting out for me without that set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@548 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:17:20 +00:00
9a8902571c
Placeholder for parallel MicroManager.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@542 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 23:08:12 +00:00
1daa011387
Interval-based traversals were bleeding file handles. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@541 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 18:35:54 +00:00
1e2e78265d
Inadvertently removed interval file support in new TbLbR. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@540 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 18:15:42 +00:00
c9e9731495
More cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@539 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 17:46:52 +00:00
4036f24909
Documentation and cleanup work in preparation for parallelism.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@538 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 17:42:00 +00:00
0c76a70313
Renamed traversal by "interval" to "locusWindow"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@537 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 02:26:08 +00:00
9a299c11d3
Oops, typo and build problems. FYI, fixing typos is better than packing...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@536 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-25 01:37:17 +00:00
ce470702fc
consistency with java naming conventions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@535 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:44:48 +00:00
bfce0c93ab
removing bad file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@534 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:40:04 +00:00
05c6679321
Enabled ReduceByInterval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@533 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:39:44 +00:00
ee2f022c71
Make new TraverseByLociByReference the default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@532 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:50:11 +00:00
e50ae97fe1
Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@531 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:40:21 +00:00
dd408a2a9a
First draft of actual pooled EM caller.
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Produces sane looking output on region of 1kG pilot1:
CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084
Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@525 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 13:42:15 +00:00
13d4692d2e
1. Added a by-interval traversal.
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2. Added a shell for the indel cleaner walker (it's currently being used to test the interval traversal).
3. Fixed small bug in downsampling (make sure to downsample the offsets too)
4. GenomeAnalysisTK.execute => anyone object to my change to "instanceof" instead of trying to catch a ClassCastException (yuck)?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@524 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 04:33:35 +00:00
bd4cacb832
Added code to make a read group and sample name for BAM files that don't annotate them on reads. The defaults for both are now the filename, but this may be shortened in the future.
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The sample name for a read can be retrieved with the command:
read.getAttribute(SAMTag.RG.toString());
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@518 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 00:31:00 +00:00
635bfd8604
Added a little bit of hack to get the header back to the walker by initialization time, which was before sharding in the last version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@516 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 21:07:11 +00:00
0208d201c7
Forgot this in the last commit...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@515 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:47:22 +00:00
3dc2afd7ab
Added the ability to get a merged header in a LociByReference traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@514 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:34:52 +00:00
282f1d88b8
Make the operation 'read from the iterator and place on the queue' atomic with respect to hasNext(), next().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@513 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:16:26 +00:00
8c13940c5a
A lot of changes to support by-read sharding and some from debugging of the by loci traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@511 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 19:03:14 +00:00
3d7575bbb8
Oops...omitted walker.initialize().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@504 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:35:28 +00:00
1bf4d040d8
Increase default shard size from 5 to 100000.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@494 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:29:44 +00:00
3af66a462e
Make PrintLocusContextWalker less verbose.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@493 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:28:02 +00:00
4cafb95be8
TraverseByLoci / TraverseByLociByReference suffered from the same sam-triggered off-by-one (?) bug as TraverseByReference; it was just less obvious here because these versions don't shard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@491 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 15:48:20 +00:00
cb2f621d01
reverting accidental commit of change to shard size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@490 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:33:28 +00:00
b820130dce
* added ability to load multiple BAM files from command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@489 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:28:08 +00:00
5abfc7d079
Added an argument ('extended' or 'ext') that outputs the four-base probs in a long format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@485 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:27:26 +00:00
521e202a10
updated interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@482 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:07:20 +00:00
55ca272919
reimplemented; now implements Genotype interface instead of AllelicVariant
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@481 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:06:42 +00:00
eafb4633ba
Temporary workaround for samtools index bug: there seems to be an off-by-one error. Will file bug report.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@470 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 23:14:41 +00:00
f2f9fa3ed4
doc added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@464 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:43:25 +00:00
d639ec3776
Remove some copied code to make sure the traversal engine stays in sync with the locus context provider.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@463 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:41:56 +00:00
50ae1763f7
Support for -continue_after_errors flag in the validating pileup walker in case you want to see errors as they arise, rather than aborting greedily
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@461 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:13:11 +00:00
ee5ab9536f
trivial checking / flagging issues to enable testing of merging iterator performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@460 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:11:59 +00:00
dbf2344cef
Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@459 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 01:27:36 +00:00
01be8f09e3
Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@457 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:17:25 +00:00
e5c80e59dc
fixed the case when you're not seeking, it didn't initalize
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@456 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:16:03 +00:00
165e504d1c
Turn on new TraverseLociByReference is now only dependent on the -et flag. REGION_STR does not matter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@454 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 19:45:47 +00:00
12e1f192c4
Fixed a bug in this code where it would eat reads that didn't start at the beginning of the provided interval. This should fix / help fix Kristian problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@453 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:42:00 +00:00
835f1067d8
added isHom() and isHet() queries to the Genotype interface (with the obvious meaning)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@452 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:41:39 +00:00
d35a542bb9
* fixed bug where the merged header was not being set on the read (although the read group was)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@445 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 12:53:07 +00:00
0d324354ae
separate interface for genotypes as opposed to (population) allelic variants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@443 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:55:16 +00:00
7261787b71
Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@438 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:38:28 +00:00
e70aecf518
bug fix, but important
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@437 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:07:20 +00:00
67ea66c866
Bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:12:18 +00:00
1edfe48194
Better debugging output with .debug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@433 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:09:18 +00:00
9cc808104e
Fixed subtle bug in permitting EXPAND_WINDOW to be > 1. We now use the right window size so we avoid including empty hangers. There's still a rare bug to sort out, which occurs in the case where a read with an indel can generate empty hangers.
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Also cleaned up the debugging output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@432 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:08:26 +00:00
180ff13290
Added a bunch of changes to support the new MicroManager code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:29:38 +00:00
12407b5b1a
Deleted the old file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@427 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:55:01 +00:00
6db9127f90
Added changes to shattering, refactored SAMBAM into SAM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:52:56 +00:00
24722a442e
Slight code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:21:36 +00:00
13b0995d54
Adding an iterator that bounds the number of reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@419 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:18:31 +00:00
72a3d84ed2
General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:13:10 +00:00
0629f79049
Moved fasta support files into their own package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 18:13:23 +00:00
eb4b4a053b
A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:19:20 +00:00
30121534ed
Outputs the secondary bases and quals (if available) in verbose mode. Prefixed with the tag 'SQ='.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@398 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:58:28 +00:00
8b2c2e677b
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@396 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:43 +00:00
1cee7948ab
Added lots of assertions to check for problems.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@395 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:19 +00:00
794360c410
Added verbose option to show mapping qualities and base qualities as ints!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@394 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:54:48 +00:00
cc75e8f712
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:58 +00:00
8e6093d5a5
remove mom/dad/kid cmd line arguments that were needed for mendelian walker; now we can use generic track binding!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@389 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:45:34 +00:00
887adcfc7f
Some minor fixes to the last check-in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:24:51 +00:00
f2d0d73309
removed old shard strategy code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@386 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:13:45 +00:00
dd604799dc
Added some new code for shard support over reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@385 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:11:43 +00:00
e91a429c58
A class to print out as much context about the given locus site as is possible. Useful for testing traversal engines -- run old and new code across a given region and diff the output to make sure they have the same context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@383 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 15:29:55 +00:00
b4136b6d6e
a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 04:49:19 +00:00
756e6c61d8
Strictness args are presented as lowercase in the help, but only accepted if uppercase. Changed help to list the valid arguments in uppercase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@376 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:50:19 +00:00
c7777d46d6
* re-enabled setting of sequence dictionary information on GenomeLoc
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@366 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:44:14 +00:00
ce72932a45
* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes
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* added basic unit test for GenomeLoc
* fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:25:17 +00:00
608a66e6ab
TbyLocibyRef previously didn't seem to support traversals with no interval specified. Put in a temporary fix until the threaded approach is in place.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@363 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 22:14:06 +00:00
c2669021b8
Cleanup, and support either by-interval traversals or full traversals in data source-backed code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@362 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 22:09:01 +00:00
2322bb7d86
Workaround: use a single ReferenceIterator for an entire micromanaged traversal. We'll have to
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do something about ReferenceIterator thread safety later.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@361 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 20:50:28 +00:00
95753e1b34
Should've been calling queryOverlapping in locus mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@360 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 20:22:04 +00:00
17b3d5b554
New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@355 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 22:04:59 +00:00
aaron
hanna
depristo
ebanks
jmaguire
kcibul
kiran
asivache