641afc4e76
fix a crash in the event that the input file has no read groups!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@714 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:41 +00:00
d8c1b010f1
Fixing the naming of the function I checked in earlier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@713 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:10 +00:00
5858f20902
Documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@712 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:58:43 +00:00
68c9455c0f
Moved the base complement method to BaseUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@711 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:57:48 +00:00
3761c0900b
Added Bustard vs. Four-prob percent bases consistent output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@710 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:01:41 +00:00
7a1f85ff86
option to print out the indels found by the cleaner to a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@709 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:50:08 +00:00
b62bddee42
The header was never being set.
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Added this hack for now and will alert the authorities ASAP...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@708 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:18:51 +00:00
959cf09d4b
Removed some debugging print statements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@707 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:12:42 +00:00
2f42a643a8
A new, much simpler (and now, complete) driver program for four-base probs. Serves as a model for anyone who wants to write their own driver program that trains and calls with data from a different source than the raw Illumina data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@706 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:58:22 +00:00
5824dea0c1
Trains and calls a read at a time rather than a base at a time (which, given it's name, it should have done in the first place)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@705 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:57:00 +00:00
e4770885fd
The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:55:49 +00:00
fdd123fe16
A parser the raw Illumina data. Allows one to arbitrarily jump from one tile to another.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@703 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:53:07 +00:00
7aa90757ac
Moved the iterators over to the StingSAMIterator interface. This will help us ensure that iterators that need to be closed get closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@702 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:18 +00:00
6d98234555
Holds raw intensities, sequence, and quality scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@701 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:03 +00:00
241de0b235
A class that implements multiple training strategies and presents the training data in a common form.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@700 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:51:29 +00:00
64c65c7751
New methods to generated compressed SQ quality elements in line with the SAM spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@699 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:50:31 +00:00
c3b2c66911
The GATK doesn't need the rest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@698 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:20:45 +00:00
0215905bb6
Added an adapter class, that will adapt plain iterators and closeable iterators of SAMRecords into STingSAMIterators. Also unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@697 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 15:17:32 +00:00
5dda448ae0
1. Add printouts for the cleaner
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2. First pass at the entropy interval walker (still needs work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@696 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:59:48 +00:00
80c13f7127
Added a getter for command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@695 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:55:52 +00:00
307c6e4ecf
Oops. Forgot to add new file to svn.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@694 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 00:52:30 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
7b59f63f12
and don't forget to close sam writer after we are done...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@692 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:46:36 +00:00
de0cce87ea
new optional arg added that allows to specify a separate bam file to send all piles that fail to realign to; plus minor fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@691 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:24:23 +00:00
12ae3a22b6
Break locus context data access providers into modular components in preparation for traverse by loci.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@689 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 18:51:16 +00:00
7084ecdeb6
a few changes; checked in to allow debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@688 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 15:50:48 +00:00
5b47c5ab6c
fixing kiran's busted build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@686 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 21:29:04 +00:00
4f2c8bf0a3
Fixed an import statement that broke when all the files were moved to this directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@685 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:43:16 +00:00
cedc4c9ccb
Refactored into oblivion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@684 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:33:07 +00:00
4e4767e5de
Moved to org.broadinstitute.sting.secondarybase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@682 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:43 +00:00
219eb60716
Added newly-required documentation to arguments so that build can complete successfully.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@681 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:10 +00:00
688358190c
Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:24:18 +00:00
8079acb1d3
basic step0 implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@679 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:49:39 +00:00
57ecb7fbf1
Nicer reporting functions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@678 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:30 +00:00
ee99320c83
Removed at Mark's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@677 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:21 +00:00
f1de3d6366
Minor tweaks to how probs are supplied.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@676 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:47:41 +00:00
095dacd154
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@675 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:50 +00:00
758f8aa89b
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@674 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:34 +00:00
1518f8f9bf
Update training data creation in CovariateCounterWalker to output much smaller files by counting the number of occurences of each data point combination rather than outputting a line for each data point (i.e. each base). Also fixed bug in LogisticRecalibrationWalker where a null SAMHeader was being pulled from a function that is now marked deprecated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@673 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:23:14 +00:00
4c12df372c
Dumb, dumb bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@672 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:21:33 +00:00
6e69193e3c
Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@671 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 18:52:42 +00:00
630066cc0a
1. Merge LocusWindows whose reads overlap.
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2. Fix bug (we weren't clearing the "to emit" list)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@670 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 17:33:23 +00:00
9f942fdfa0
Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine.
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Also fixed a bug where we'd exception-out if we didn't provide a interval region.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:33:55 +00:00
c4d89997ca
put in a dummy sample_name so it'll compile
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@668 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:42 +00:00
c8d7223789
do pooled calling properly for 1kg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@667 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:13 +00:00
313a6d0fb5
lots of changes to facilitate calling indels and 1kG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@666 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:11:42 +00:00
add7b6cf65
add sample_name to constructor, misc bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@665 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:10:17 +00:00
0267ccae7f
add code for computing indel genotype likelihoods
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make reference lods negative
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@664 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:09:29 +00:00
11723fbcc2
added method indelPileup. Generates a pileup of indel alleles given reads and ofsets (as from a locus walker).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@663 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:08:24 +00:00
ee9077fc69
LocusIterator iterated through LocusContexts, which was fine until now when we need something
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that iterates through loci (GenomeLocs). Rename LocusIterator to LocusContextIterator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@662 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 13:54:57 +00:00
jmaguire
aaron
kiran
ebanks
hanna
asivache
depristo
kcibul
andrewk