752928df94
Switch to better mechanism for supplying a default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 01:22:01 +00:00
dc944ec69b
First stage of ROD plumbing for MicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@614 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 23:26:21 +00:00
5136724884
Added code to the schedulers, one step closer to turning on the new reads traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@613 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:36:25 +00:00
9c0b81e946
Default flags to 'not required'.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@612 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:09:49 +00:00
072808858e
added COUNT_CUTOFF arg: it is nor possible to tell the code to try to realign all read piles over trains of nearby indels with at least one indel observed in COUNT_CUTOFF or more different alignments (set the arg to 1 to realign around all indels); also, some diagnostic printouts added to the output (time spent on loading the reference, time spent on scrolling through the input bam file, counts of discarded reads)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@611 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:59:33 +00:00
1fe8155111
Some critical fixes for cases where argument values directly abut argument names
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and for arguments with missing short names.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@610 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:47:34 +00:00
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
62e7e46754
Miscellaneous cleanup. Better display of help output. Better exception subtyping. More thought-out access routines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@608 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:16:01 +00:00
5be75e0ae6
First version of indel cleaner walker that works on intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@607 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 20:20:48 +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
98f4920739
Added BCEL and some basic instrumenation code to the test library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@602 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 17:18:23 +00:00
bfd6dfe36c
Added real-world tests and tests for conditional validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@601 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 13:38:46 +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
2ee9374975
Check for proper error output in case of boolean args with parameter specified.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@599 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:08:48 +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
ec0261275b
Lots of command line argument validation. Catches all common validation problems, including missing required arguments, invalid arguments, and several types of misplaced argument value errors.
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Still pending:
- Help system.
- Mutually exclusive arguments.
- Design includes too many classes per file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@597 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:08:00 +00:00
70afda12c4
Cut the test time down
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@596 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:05:51 +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
6550fe6f97
Another pass of command-line arguments. Revised parser supports all types
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of arguments that the existing parser supports, but does a poor job with
validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@591 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 22:41:23 +00:00
8925df2e1e
More information from the duplicate combiner quality metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@590 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 21:51:01 +00:00
2b6466ea00
coverage calculator based on Gabor's Pilot 3 Coverage Metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@589 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 14:18:16 +00:00
4f2ccda56a
Interface skeleton for a new command line argument parser. Nowhere near the point of being a drop-in replacement for apache cli yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@588 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 00:11:42 +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
fd496159a8
Added convenience functions for RefHanger
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@585 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:14:40 +00:00
7ed496b859
JUnit test for RefHanger
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@584 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 20:11:14 +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
df88c4d6b0
Added some code to determine the on-genotype and off-genotype secondary base distributions (which, at the moment, is commented out).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@582 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:48:19 +00:00
e7534b292f
Optionally applies secondary base distribution priors to normal single-sample genotyper posteriors.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@581 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:36:32 +00:00
58c80d8d87
For on and off-genotype primary bases, optionally compute the concordance of the secondary bases to their expected distributions. Each genotype has slightly different profiles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@580 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:33:48 +00:00
16467ae7cf
A better (less overflow-y) implementation of multinomialProbability().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@579 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:28:16 +00:00
4f818f5c1c
Choose a random base to stick in the pileup if the 2nd-best base matches the best base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@578 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:27:37 +00:00
9800d09608
A more thorough test for multinomialProbability.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@577 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:27:05 +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
12d6edfe7c
Only prints about first contig info setting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@574 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:14:26 +00:00
1cc5e74435
More ways to access quality utils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@573 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:12:07 +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
19e4e97f21
Add tag to ignore node class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@571 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:27:34 +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
3bf3c21ddd
Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@569 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 13:54:51 +00:00
b630f2f2f1
More tables output by CovariateCounterWalker AND made CovariateCounterWalker and LogisticRecalibration aware of positive and negative strandedness of data which changes the regression output significantly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@568 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 01:22:50 +00:00
f7a877bfeb
Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it.
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Please use this instead of throwing a plain runtime exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@567 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 22:09:41 +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
hanna
aaron
asivache
ebanks
depristo
kcibul
kiran
andrewk