aece7fa4c7
a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2057 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 16:50:01 +00:00
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
768f865035
Bulletproofing code. If errors are encountering during the run, turn them
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into JDK exceptions whenever possible instead of random core dumps. Don't
allow negative values for most of the 'bwa aln' input parameters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2049 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-14 22:57:16 +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
b7097a8db9
Build aligner as separate jar file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2044 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 22:29:29 +00:00
f5818c0cda
Fix max edit distance to ensure interface similarity between our aligner and
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'bwa aln'.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2043 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 22:18:56 +00:00
52494d8176
cleanup of SNP selector -- ready for some additional testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2042 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 21:46:31 +00:00
8eff1cc436
Extract and include only the Tim Fennell-approved parts of picard private.
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Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2041 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:42:33 +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
1a4d071d37
Better snpSelector, plus VCFmerge tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2022 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 22:02:57 +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
637f02f392
BWA/C changes have arrived in svn repository. Remove temporary storage from Sting repository.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2019 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 16:48:21 +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
aaron
asivache
rpoplin
ebanks
hanna
kiran
depristo
mmelgar