21729d9311
Do not print debug message when debug mode is not requested!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2056 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 20:28:41 +00:00
967215066d
The old CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2055 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 19:16:46 +00:00
eb07c7f7f8
CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2054 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 18:44:54 +00:00
4558375575
Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated.
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VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper. UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).
This is a fairly all-encompassing check in. It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout. All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.
Stage 2 of the process will happen later this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 02:41:20 +00:00
ce5034dc5d
Finally reinstate the iterator-style interface. Get rid of some scaffolding code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2052 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 02:34:19 +00:00
103763fc84
An accessor for the VCF header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2051 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-15 09:28:25 +00:00
97ed945797
Example code for a bug in the VCF implementation. See JIRA entry at http://jira.broadinstitute.org:8008/browse/GSA-225
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2050 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-15 09:27:12 +00:00
88fd762436
The -rf argument is now being used for read filter and is colliding with my walkers. Changed mine to -recalFile
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2048 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-14 19:37:46 +00:00
b05119987c
Clarified some of the comments in the individual covariates now that things have been moved around to speed up the code. In general most error checking and adjustments to the data are done per read instead of per base. This means that functionality was moved out of the covariate modules and into CovariateCounterWalker and TableRecalibrationWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2047 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-14 18:44:05 +00:00
672472789e
Added some documentation to the helper classes. Fixed an error case in TableRecalibrationWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2046 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-14 18:13:43 +00:00
15c14add4d
Repackage the aligner for better partitioning. The C aligner, for example, is now
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partitioned from the Java aligner, and both are partitioned from the more general-
purpose BWT reader.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 22:55:27 +00:00
d1b525b428
Default window size for NQS covariate is 3
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2040 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:24:27 +00:00
394c839974
Implemented NQS covariate. Extended Cycle covariate to handle 454 and SOLID reads. Added a Primer Round covariate for SOLID reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2039 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:22:21 +00:00
bf451873ff
1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction
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2. Fix for Kiran: allow UG to call SNPs at deletion sites; we'll add an annotation to the VariantAnotator for deletions at the locus (next week).
3. Added integration tests for joint estimation model
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2038 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 18:02:18 +00:00
1be36ca959
Bug fix: when cleanedReadIterator is initialized, it gets immediately set to the contig of the first cleaned read; when the first uncleaned read coming in is on the lower contig, this would trigger 'readNextContig' with that lower contig as an argument. As the result, the whole cleaned reads file would be read through the end and no cleaned reads would be ever seen by the code afterwards. Now we do not call readNextContig if the (uncleaned) read's contig is lower than the current contig already loaded into cleanedReadIterator. the 'readNextContig' method now also throws an exception if requested contig is less than the currently loaded one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2037 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 15:41:26 +00:00
b1376e4216
structure refactored throughout for performance improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2036 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 15:41:09 +00:00
cff31f2d06
comments for eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2035 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 14:19:31 +00:00
234bb71747
changed the toVariation() method to take a reference base, instead of using the reference base loaded from the underlying data source (if it was reference aware). Also changed some isVariant() methods which weren't using the passed in ref base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2034 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 06:54:38 +00:00
902cf84448
Bug fix: if the most likely allele frequency is 0, don't make a variant call (even if the Qscore for AF=1/n > threshold)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2033 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 04:10:32 +00:00
555fb975de
1. Print out allele frequency range (from joint estimation model only).
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2. Don't print verbose output from SLOD calculation (it's just a repeat of previous output).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2032 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 03:59:13 +00:00
72825c4848
A walker that generates a table of secondary base counts in a bam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2031 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 02:11:23 +00:00
7c386fa428
Another case of reordering of read groups blowing up checksums.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2030 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 00:07:35 +00:00
8145ed4672
Take 2, updating picard with bug fix for bam files containing no reads.
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Just stomped on the existing md5s because that's what Eric told me to do.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 22:52:08 +00:00
61b5fb82ce
2 major changes:
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1. Add dbsnp RS ID to VCF output from genotyper; to do this I needed to fix the dbsnp rod which did not correctly return this value.
2. Remove AlleleBalanceBacked and instead generalize the arbitrary info fields backing VCFs (and potentially others) in preparation for refactoring VariantFiltration next week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2028 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 22:51:49 +00:00
3742a05760
Now can read E2 or SQ tag.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2027 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 15:18:21 +00:00
c3c001e02e
cleanup of the traversal output code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2026 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 06:18:10 +00:00
0922400ca9
Don't try to calculate ratios when DoC is zero (which happens when calls are made by an LD-aware genotyper)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2025 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 02:51:44 +00:00
697d7e02c8
Remove the lazy initialize functionality. When no calls are made by the genotyper, we still want a vcf file to be output with valid header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2024 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 02:14:50 +00:00
2ea85fb62b
Fix some problematic command-line argument naming and descriptions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2023 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 02:12:26 +00:00
0c2a957ae0
Better configuration support. Now supports everything that people have expressed interest in except edit distance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2021 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 20:54:49 +00:00
6c9f86bb4d
Removed unnecessary output and added debugging print() routine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2020 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 18:37:36 +00:00
578dcc54a4
Don't create a record if ref=N
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2018 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 04:32:17 +00:00
8406325247
New Picard is breaking one of the integration tests.
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Revert until we find out whether the cause is legit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2017 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 03:59:32 +00:00
499e7d1d75
Push forward some more delicate merging routines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2016 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 03:07:34 +00:00
bae4d3f7ea
Updated Picard with fix for Doug Voet. Thanks Alec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2015 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 02:01:08 +00:00
2e4782f202
Command-line arguments for SamReadFilters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2014 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 23:36:17 +00:00
a13cbe1df0
The refactored recalibrator now passes the integration tests as well as my own validation tests. I'm ready to have other people start jamming on the files. I'll make an updated wiki page soon. The refactored recalibrator is currently a bit slower than the old one but there were a lot of great, easy ideas today for how to improve it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2013 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 22:20:06 +00:00
2cf9670d1e
Allow users to directly specify filters from the command-line, applicable to
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any walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2012 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 18:40:16 +00:00
6a37090529
Output changes for VCF and UG:
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1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 16:31:31 +00:00
1e7ddd2d9f
Added a validateOldRecalibrator option to CovariateCounterWalker which reorders the output to match the old recalibrator exactly. This facilitates direct comparison of output. Changed the -cov argument slightly to require the user to specify both ReadGroupCovariate and QualityScoreCovariate to make it more clear to the user which covariates are being used. Some speed up improvements throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2010 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 15:55:56 +00:00
7e30fe230a
oops, missing file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2009 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 13:25:18 +00:00
d316cbad4c
VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 13:24:58 +00:00
f9819d5f13
a little clean-up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2007 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 06:18:34 +00:00
2ed423ed56
print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2006 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 05:57:01 +00:00
c9c3cf477a
Based on feedback from Kiran, we know uniquify sample names as sample.rodName (instead of sample.1, sample.2, ...)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2005 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 02:41:37 +00:00
2fa2ae43ec
Enough people have found this useful, so...
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Moving Callset Concordance tool to core and adding integration test.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 20:59:18 +00:00
3793519bd4
-Added convenience method to VCF record to tell if it's a no call and have rodVCF use it before querying for info fields
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-Don't restrict info fields to 2-letter keys
[about to move these to core]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 20:52:51 +00:00
740a5484c4
Added some documentation to the code, mostly especially to CovariateCounterWalker but various comments added throughout. Also changed the HashMap data structure to accept an estimated initial capacity. This had a very modest improvement to the speed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2001 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 20:13:56 +00:00
74751a8ed3
-Some minor fixes to get accurate vcf record merging done
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-Improvement to snp genotype concordance test
And with that, it looks like I get revision #2000 .
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 06:40:55 +00:00
ab705565cf
Completely refactored the Callset Concordance code. Now, it takes in VCF rods and emits a single VCF file which has merged calls from all inputs and is annotated (in the INFO fields) with the appropriate concordance test(s).
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Still needs a bit of polish...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1999 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 05:03:13 +00:00
bc6f24e88f
Added VCFUtils which contains some useful VCF-related functions (e.g. ability to merge VCF records).
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Also, various minor improvements.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1998 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:53:32 +00:00
cff645e98b
convenience method to deal with genotypes that are unsorted (e.g. CA vs. AC)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1997 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:45:49 +00:00
7fde6c0bf4
One more output tweak.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1996 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:42:55 +00:00
00a7113d7a
Tweaks to formatting of output table.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1995 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:33:36 +00:00
7ce0df76f8
Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1994 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:25:39 +00:00
d07f3bb6f6
Added methods to get strand bias and to test if record has allele freq or bias fields set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1993 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:20:35 +00:00
3313b0ddb4
Fixed a minor bug where the lodThreshold wasn't being printed in the header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1992 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:51:36 +00:00
95d381efe2
Optionally computes the error rate using the best base and a random base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1991 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:47:34 +00:00
567f5758d2
Optionally lists read depths by read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1990 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:39:19 +00:00
a679bdde18
FindContaminatingReadGroupsWalker lists read groups in a single-sample BAM file that appear to be contaminants by searching for evidence of systematic underperformance at likely homozygous-variant sites.
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Procedure:
1. Sites that are likely homozygous-variant but are called as heterozygous are identified.
2. For each site and read group, we compute the proportion of bases in the pileup supporting an alternate allele.
3. A one-sample, left-tailed t-test is performed with the null hypothesis being that the alternate allele distribution has a mean of 0.95 and the alternate hypothesis being that the true mean is statistically significantly less than expected (pValue < 1e-9).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1989 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:36:39 +00:00
2225d8176e
A convenience class for maintaining a dynamically growing table of values with access to the elements by named row and column identifiers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1988 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:34:35 +00:00
21c5f543fa
Fix sharding bug -- loci to which >100,000 (= 1 shard) reads are assigned an
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alignment start will confuse the sharding system and cause it to return duplicate reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 14:27:26 +00:00
84ba604611
Sequential quality score calculation is now in place in the refactored recalibrator and matches the quality scores calculated by the old recalibrator exactly; at least on the small sets of data used so far. Validation, documentation, and optimization work is on going.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1985 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-07 15:55:16 +00:00
bf1bc94060
Fixes for PooledConcordance bugs and lack of safety checking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1984 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-07 01:54:10 +00:00
66d4a995e6
Initial check in of refactored Recalibrator. The new walkers are called CountCovariatesRefactored and TableRecalibrationRefactored. More work is needed to finish up the sequential calculation and to document the code sufficiently. These files are not ready to be used by other people quite yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1982 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 22:33:55 +00:00
6fdfc97db6
Added optional field DP to VCF output for Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1981 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 20:03:22 +00:00
0a55fa5bb1
Completely refactored the Genotype Concordance module(s).
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Now PooledConcordance and GenotypeConcordance inherit from the same super class (and can therefore share data structures and functionality). Also, they now use ConcordanceTruthTable to keep track of necessary info.
GenotypeConcordance passes integration tests.
PooledConcordance needs to be finished by Chris.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1979 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 16:27:16 +00:00
d549347f25
Refactored GenotypeLikelihoods to use an underlying 4-base model.
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It needs to be modified a bit and then hooked up to a pooled model, but that is now possible.
At this point, there is no difference to the Unified Genotyper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 21:59:25 +00:00
4d3871c655
don't flush anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1977 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 19:11:51 +00:00
aacd72854f
a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.
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Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1). Updated and checked BamToFastqIntegrationTest MD5 sums.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 05:26:33 +00:00
43c3ee61d5
Fix minor mapping quality bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 14:33:23 +00:00
a545859c62
Joint Estimation model now emits a reasonable slod
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1969 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 21:12:42 +00:00
11d950abe0
No longer allow the lod_threshold argument - use confidence instead.
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Have UG output qscores in all cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:18:51 +00:00
2fb45dbd73
Make window size a command line argument
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:13:35 +00:00
55f61b1f88
Bug fix in adjustment of the shift position.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:08:11 +00:00
5d5dc989e7
improvements to VCF and variant eval support of VCF -- now listens to the filter field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1963 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 12:09:30 +00:00
c63af32fc7
The BWA/C bindings were triggering the local aligner to repeatedly reload the
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ref genome. Make sure the reference genome is cached.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 00:01:55 +00:00
3a33401822
2nd stage of the genotyper output refactoring is complete.
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Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 22:43:08 +00:00
ba67c7f02b
added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 21:09:18 +00:00
b71b66bd88
the underlying parameter is a float so we need to use Float.valueOf() instead; Noticed by external user Hou Huabin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1958 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 20:22:25 +00:00
5a510e6d98
New PackageUtils interferes with the packaging utility. Revert until Aaron and
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I can get together to make this work.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1957 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 19:14:14 +00:00
de6ae51f7e
Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.
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A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 06:02:41 +00:00
1896f334d9
Fixed collection of bugs in reads aligning to multiple locations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1955 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 04:02:09 +00:00
af6d0003f8
-Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out).
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-Make rods return the appropriate type of Genotype calls from getGenotype().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 05:35:47 +00:00
b95165e39c
Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 00:33:18 +00:00
4b0796ba58
After fixing a few glitches and bugs, this version finally works as intended
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1952 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-31 04:59:58 +00:00
7d0ac7c6f2
Fix for long-term VariantEval bug plus new intergration test to catch it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1951 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-31 00:00:33 +00:00
ea8d5c7077
Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1949 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 17:50:51 +00:00
a3da475c88
Documentation and cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1946 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 15:40:28 +00:00
2d15891719
Created walkers for alignment, validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1945 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 15:04:07 +00:00
51fffc7f69
Comments for Ryan (which also apply to ReadQualityScoreWalker).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1944 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 14:44:04 +00:00
ccd7440730
We can actually make this a bit simpler (and faster)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1943 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 04:21:03 +00:00
1b6333e4ab
Enough people have asked for this that it just needed to get written.
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One can now split up any number of sets into an N-way Venn (although it doesn't check for discordance in the calls, so you'll still want to use SimpleVenn for 2-way comparisons).
Wiki docs are updated.
To do: update to use Ryan's generic hash map when it's ready for public use.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1942 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 04:08:45 +00:00
4bdb5b03bd
tell UnifiedGenotyper to return calls at all bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1941 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 03:10:44 +00:00
4ee1d6f733
-Have the calculation models determine whether a call passes the lod/confidence thresholds (as opposed to returning everything and letting the UG decide); this way, walkers which call map() will get only the good calls.
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-Do the right thing in all models for all-base-mode (for Kiran).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1940 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 02:35:51 +00:00
64ac956885
Okay, I caved in:
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CallsetConcordance now gets possible concordance types by looking at classes that implement ConcordanceType instead of having them hard-coded in.
Thanks to Kiran this was pretty easy...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1939 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 00:32:26 +00:00
1f0d852a48
Fix bug where alignments with indels would be busted because bwa reverses
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the read bases to undo a previous read base reverse that doesn't occur in the
libbwa codepath.
Also fixed some memory management issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 21:33:13 +00:00
e3b4d4cbed
Genotyper reimplemented. Does the same thing, at least for now, but internal data structures redesign enables collecting various statistics for indel-containing/reference-matching reads. The statistics are not yet used by the caller itself to make a better judgement w.r.t. the validity of the calls it makes, but they are now printed into the output stream (--verbose). The statistics (for both normal and tumor) include: indel observation count/total coverage, av. number of mismatches per indel-containing and per ref-matching read, av. mapping quality, av. mismatch rate and av. base quality within an NQS windoew around the indel, numbers of indel and ref observations per strand.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1936 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 19:09:16 +00:00
f04b80d7db
Fixed epic memory leak.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1934 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 16:32:43 +00:00
2b96b2e4e7
better multi-sample integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1933 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:51:51 +00:00
asivache
rpoplin
ebanks
hanna
kiran
depristo
aaron
mmelgar
jmaguire