17cc484dbd
Revert "ReduceReads ref bases are now output as '='
...
Reducing the reference bases to '=' results in an extra compression of 13% on average. The GATK is not ready to handle files with '=' bases, and the decision was to implement this a an engine support, not a part of ReduceReads.
2011-11-01 16:35:07 -04:00
76c32f5409
Revert "Compressed read group information"
...
We decided not to compress read group information because read groups should be universally unique. The gain of 3% compression was not worth it.
This reverts commit 79f1c3b70de240d8060ecb9a86d2f1d4ff2a8efb.
2011-11-01 16:33:21 -04:00
74b018a1f3
Minor fixes to docs
2011-10-31 21:41:43 -04:00
b51c36abb3
TEST: equal '=' base test implementation
2011-10-31 18:01:22 -04:00
31ee5432c5
Merged bug fix from Stable into Unstable
2011-10-31 14:56:59 -04:00
cdde32acbd
Merged bug fix from Stable into Unstable
2011-10-31 14:21:15 -04:00
f62af0291b
Check for invalid VCF records (not enough tokens) instead of assuming they are there.
2011-10-31 14:09:51 -04:00
bed0acaed4
nWayOut now adds PG tag to the header as it should. Also, additional hidden option added: keepPGTags. If invoked, IndelRealigner PG tags from previous runs (if any) are kept in the header and the new PG tag is simply added, instead of overriding them
2011-10-31 12:28:28 -04:00
7a8e49154d
Fixing contracts
...
forgot to rename the variables in the contracts. This should resolve Bamboo failures.
2011-10-31 09:21:19 -04:00
ab4f58a5e9
A base for a test walker for reduce reads
...
this walker allows general testing on reduce reads given two bam files to make sure the reduce reads are not screwing up the format. This is just the base of the walker, the tests need to be implemented independently inside the framework.
2011-10-30 22:26:16 -04:00
e220507ff9
Compressed read group information
...
Adding another 3% reduction in file size by compressing the read group ID.
2011-10-30 21:09:06 -04:00
389380a590
ReduceReads ref bases are now output as '=' to save space
...
Restructured the sliding window framework to manipulate a wrapped version of the SAMRecord that contains information about the reference.
2011-10-30 12:04:39 -04:00
dbd8c25787
No more R resources in the DPP
...
updating the DPP to conform with Analyze Covariates changes.
2011-10-28 16:57:01 -04:00
e25d40882a
Swapping Thread.sleep(0) with Object.wait(0) caused Queue to lock up. Thanks to rpoplin for pointing it out.
2011-10-28 15:51:03 -04:00
0ca7428e76
Allow processing of empty intervals, but warn user when this case is encountered.
2011-10-28 12:12:14 -04:00
649dfe98f0
Add VCF header for any expressions that are requested
2011-10-28 10:22:19 -04:00
8b1a62da27
Adding unit test to cover overlapping intervals from the same source with the intersection rule.
2011-10-28 09:59:43 -04:00
057a79f598
This argument should be annotated as @Input
2011-10-28 09:44:49 -04:00
4ba7c0cecd
Moving to private
2011-10-28 09:29:28 -04:00
1bdd76c2f2
These tools now use the IntervalBinding system to handle intervals instead of doing it all manually
2011-10-28 09:28:12 -04:00
6ba08a103d
Empty ROD files should generate an exception when used for creating intervals. Moved some now obsolete files to the archive as the realigner will now read all target intervals into memory.
2011-10-28 09:23:25 -04:00
3d04bb5608
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-27 23:55:18 -04:00
19e27d4568
Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
2011-10-27 23:55:11 -04:00
cafc245a43
For some reason, a class of Codecs (including TableCodec) require that a GenomeLocParser be passed in to do the position processing. Why can't they just return a Feature with chr, start, stop? Isn't that the right thing?
2011-10-27 23:54:28 -04:00
cbc43683ee
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-27 20:54:18 -04:00
8907e42007
First fully functional implementation of ValidationSiteSelectorWalker. User gives a) a set of input variants, b) a desired number of output variants, b) Optionally, a set of samples which will restrict sites to be polymorphic in those samples, c) a frequency selection mode: either uniform (no AF matching), or matching AF so that output sites mirror the input AF spectrum as closely as possible.
...
More testing is needed and docs need improving but so far all functionality seems up and running
2011-10-27 20:53:48 -04:00
ccfd853b34
Added further integration tests for rod-based intervals that deal with more complex cases. Good call by Mark to test the empty VCF example because we were failing on it; fixed.
2011-10-27 20:43:50 -04:00
49b616b8e6
Outputting compressed read names
...
In an attempt to minimize file size, read names are compressed to a number. Reads with the same name will have the same number. Consensus reads will have a C in front of the number. Tests show an average 10% reduction (extra) in file size.
2011-10-27 16:59:58 -04:00
648a17a30b
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-27 16:27:30 -04:00
1ecd08a296
Better docs for VariantsToPed
2011-10-27 16:27:19 -04:00
c2f343773e
Oops, working too quickly last time. This is the proper fix for the potential NPE in the equals() test.
2011-10-27 15:32:08 -04:00
4d0e34109f
Compacting pdfs when running under R 2.13+.
2011-10-27 14:51:56 -04:00
b80d407dc7
No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
...
Other minor cleanup.
2011-10-27 14:17:07 -04:00
8c4dbce6d8
Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.
2011-10-27 13:58:19 -04:00
4a7e6fee3f
Remove support for BED file interval parsing in the GATK; it should all go through Tribble now. IndelRealigner no longer supports unordered interval input (which shouldn't have been used anyways). Temporarily commenting out serialization of arguments so that tests pass; this whole piece will be deleted soon anyways.
2011-10-27 13:38:08 -04:00
f7df8bdecc
Merged bug fix from Stable into Unstable
2011-10-27 11:31:17 -04:00
41ddc7bce7
Make sure we output a full stack trace when we encounter Tribble error messages on VCF header merge.
2011-10-27 11:30:04 -04:00
9ca2828547
Bug fix for multiallelic records: When combining SNP and indel record the original alleles are reference padded in one case but not in the other. Added missing normalization of the haplotype likelihood matrix. Unfortunately turning the banded approach off for now because it kills specificity.
2011-10-27 09:51:40 -04:00
44f905b5e5
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-26 23:31:11 -04:00
68283b1651
Fixing docs and adding GATKdocs for the new interval functionality
2011-10-26 22:14:43 -04:00
c9978316a3
Merge branch 'FragmentUtils'
2011-10-26 19:51:49 -04:00
add9ad97ec
No scatter gather for VQSR or ApplyVQSR.
...
These walkers should not be scatter gatherable. Annotating them accordingly so that Queue doesn't allow a less than knowledgeable user to try and scatter/gather VQSR.
2011-10-26 16:35:44 -04:00
6b3aa7ce62
Script to evaluate VQSR on reduce reads
...
This script makes calls and recalibrates a list of reduced BAMs and a list of non-reduced BAMs using the current best practices for exome calling (to be extended to WGS as well).
2011-10-26 16:35:44 -04:00
74aeb22eeb
Merged bug fix from Stable into Unstable
2011-10-26 15:57:30 -04:00
86871bd1e3
Throw a UserException in the BQSR when there is no data instead of creating an empty csv file
2011-10-26 15:56:41 -04:00
034a997d07
Generalized Reads -> Fragment calculation
...
-- Supports ReadBackedPileup -> FragmentCollection as before
-- Added support for List<SAMRecord> -> FragmentCollection for Ryan's haplotype caller
-- General cleanup, renaming, move to separate package, more extensive unit tests, etc.
-- Added toFragment() function to ReadBackedPileup interface
2011-10-26 15:54:38 -04:00
2f21b6ecfb
Removed debugging output
2011-10-26 15:50:20 -04:00
b39fcb1bea
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-26 15:44:25 -04:00
b6ce6ed3f8
Go around the ROD system for now so that we can just call decodeLoc() for efficiency. Noted that we should go through the ROD system once it gets cleaned up. This means that currently gzipped files are not supported with -L.
2011-10-26 15:42:53 -04:00
3273c20c98
Added integration tests for Tribble-based intervals and fixed up some of the other tests based on some method changes.
2011-10-26 15:29:18 -04:00
Mauricio Carneiro
Eric Banks
David Roazen
Andrey Sivachenko
Khalid Shakir
Guillermo del Angel
Mark DePristo
Matt Hanna
Ryan Poplin