93211c1cd8
template for windowmaker utility -- total non-functional
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@625 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:13:03 +00:00
71e8f47a6c
boundQual function for capping qual values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@623 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:04:18 +00:00
e848f34896
countOccurances of char in string and max of a list of bytes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@622 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:49 +00:00
5a4bb76cc3
More capabilities for the pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@621 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:13 +00:00
89a26a7078
Utilities for handling duplicates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@620 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:02:24 +00:00
4f85062004
Cleanup parsing method to make it less generic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@619 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 16:21:17 +00:00
2f3ab53888
Oops. Arguments didn't load into applications with non-plugins (basically everything except the GATK).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@617 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:37:19 +00:00
4177560543
Mutually exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@616 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:27:48 +00:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
4c5f640eb7
Tweak the arguments passed to the command-line arguments parser so that it fails less often for invalid arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@560 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 14:36:27 +00:00
58b2578c44
Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@550 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 00:37:48 +00:00
b9c9dbb1d7
Added multinomialProbability method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@545 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:03:50 +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
40a2b3eeb3
Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@529 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:09:50 +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
135d3eabeb
Now only distributes 80% of the residual probability to the secondary base, 10% each to the other two bases. Nicer labelling for stringified probability distribution output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@521 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:34:43 +00:00
3cda85f2e3
New implementation of binomial probability that accurately computes values down to around 1e-237.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@520 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:32:04 +00:00
45d962e491
I understood the contig index incorrectly when I initially wrote this code. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@517 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 22:31:43 +00:00
998763950c
Oops, contig index is a zero not one based value
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@512 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 19:08:16 +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
ca66cccd2f
Privatized constructor to prevent instantiation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@506 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:45:39 +00:00
77e1e9e2f1
Added a static class to house useful math methods. All this has at the moment are methods for comparing doubles and floats, but I suggest that the bulk of our little math methods should be added here to avoid filling up Utils.java with so much random stuff.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@505 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:45:19 +00:00
6cef8bd76c
added k-best quality path enumeration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@497 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 20:26:51 +00:00
5b8502745a
Added an epsilon (1e-4) to the tertiary and quaternary base hypotheses.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@488 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:01:37 +00:00
2ac240d78b
Removed an extraneous print statement.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@487 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 23:36:36 +00:00
0149c887ff
Fixed a bug wherein the residual probability was not being distributed properly when a file had secondary probs and the best and next-best base agreed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@486 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 23:36:09 +00:00
dac76f041b
Added some methods to retreive the probability distributions of individual bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@484 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:26:25 +00:00
5b2a7c9c23
Added some methods to complement a single simple base ([AaCcGgTt]) and reverse-complement a byte-array of bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@483 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:25:33 +00:00
depristo
hanna
kiran
aaron
andrewk
jmaguire