d265397bf6
removing a reference to a unused internal Sun class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3560 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 15:27:57 +00:00
42b8a8f295
slight change in output format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3559 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 14:52:04 +00:00
32fc221ffe
Replaced pattern matched pipeline spec with annotated objects.
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Old version is no longer available.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3558 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 04:43:46 +00:00
b99a5e06f3
Added option to only consider alleles of > specific allele frequency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3557 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 02:09:35 +00:00
8a895f481f
Proper exception chaining for troubleshooting Sendu's issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3556 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 01:38:36 +00:00
8defb30796
Documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3555 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 21:31:01 +00:00
c1046653a2
Fixed handling of records where gene-names are identical (eg. as in refseq NR_030638 in chr20)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3554 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 20:00:49 +00:00
1e42984a16
Improved buffer-size arg handling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3553 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 19:59:15 +00:00
b3c3023c3c
Allows callers to handle HLA reference files as input (rather than hard-coded paths)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3552 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:56:08 +00:00
9666d47d17
ooops, debug print now removed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3550 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:07:12 +00:00
abdc8521ea
Added debug options for FindClosestHLAWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3549 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 17:52:03 +00:00
c38390eabb
Added option for min number of matches between reads and alleles required to consider reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3548 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 16:08:49 +00:00
4ab1f440c3
A new argument: --targetIntervalsSorted (boolean flag). If specified, the interval file is assumed to be sorted (duh!) and it is NOT slurped into the memory but instead traversed directly on disk as needed. If the file turns out to be unsorted, an exception will be thrown at the point where inconsistency occurs (can be late into the processing!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3547 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 16:00:22 +00:00
671ac00748
A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3546 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:54:37 +00:00
f137bf8f85
now adaptor silently skips empty lines in the underlying string iterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3545 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:35:07 +00:00
d8c963c91c
Remove PhaselikelihoodsWalker.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3544 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:21:43 +00:00
5704294f9d
HLA caller updated - now searches all (common and rare) alleles, more efficient read filtering and allele comparison runs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3543 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:14:40 +00:00
d51e6c45a7
a utility class; turns string iterator into GenomeLoc iterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3542 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 14:07:44 +00:00
7b7d3341f0
trivial refactoring: isFile renamed to isIntervalFile and made public
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3541 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 14:02:23 +00:00
c3b68cc58d
Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept
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independent while processing, and only merged back in a priority queue if necessary in a special
variant of the ReadBackedPileup. This code is not live yet except in the case of naive deduping.
Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and
not well integrated with StratifiedAlignmentContext or the walkers. Cleanup to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3540 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-13 01:47:02 +00:00
804facb0cc
Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3539 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 21:41:29 +00:00
e6d8faf293
making 'parseLocation' public static - as simple as the logic is, it's better kept in one place and I need it!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3537 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 18:19:59 +00:00
8c28be5933
Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this).
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Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3536 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 16:42:06 +00:00
22620ba95c
Adding "abi_solid" to the list of known platforms.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3534 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 13:37:19 +00:00
63ad71cca6
Fix busted code. Note for all:
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String.valueOf(byte[]) doesn't work. You must use new String(byte[]).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3533 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 05:01:48 +00:00
338bb9adf4
CommandLineProgram for measuring java I/O speeds for large plain-text or gzipped files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3532 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 21:34:37 +00:00
06fc5eecf8
Implemented TreeReducible - if num threads > 1, the output will be accumulated in memory and written to a vcf file at the end - in onTraveralDone(..). If num threads == 1, things will work as before - where vcf records are written to disk as soon as they are computed with map(..).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3530 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:57:23 +00:00
3b375cb237
Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..) - attempt 2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3529 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:54:36 +00:00
99b684ea89
Adding new support for reference data. ReferenceDataSource is a new class that manages reference data, and allows IndexedFastaSequenceFile to be a simple reader. This checkin also includes FastaSequenceIndexBuilder, which reads a fasta file and creates an index, like samtools faidx. Right now this is not enabled, because we are still working out thread safety. So the only new UI change is that GATK can be run without a fai file. Soon, we will enable 1) GATK to be run without a dict file too, and 2) both dict and fai files will be saved on disk for future program executions. For more info, see ReferenceDataSource.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3527 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:10:23 +00:00
f55f32d4ee
Bug fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3526 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 01:53:26 +00:00
ca4eab1d23
Now annotations that require reads return null if there's no alignment context, so that running without reads adds annotations only for the appropriate fields.
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Added an integration test for the read-less case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3525 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 20:36:46 +00:00
6941c81bfa
reverting revision 3522 to the old code until we fix the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3524 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 19:25:02 +00:00
dbee21a50f
Bugfixes for the case when no read groups / no samples are available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3523 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:47:05 +00:00
adc4c4e577
Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3522 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:11:43 +00:00
20167fd411
Final changes to MVC -- associates variants with regions of homozygosity in child and parents, corrects for genotype errors, and prints out a separate file with informationf or each region of homozygosity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3521 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:05:37 +00:00
fdded73861
Improved error reporting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3520 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:52:48 +00:00
4f00e265a8
quick update for a change I implemented for Ryan
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3519 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:23:31 +00:00
ad98512f6c
adding changes so that we look at the headers already loaded by the engine for samples and other VCF utils, and not create readers for each file to get them (this caused Tribble to regerenate indices if the index file can't be written to disk).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3518 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:21:12 +00:00
c1b7bcc786
Fixed handling of mitochondrial genes - added special cases such as ATT being a start codon in mitochondria. Added warning if a gene doesn't start with Met or end in a stop codon
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3517 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:15:47 +00:00
4f1181974b
Added toString() method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3516 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:12:57 +00:00
9b2fcc4711
Refactoring of the annotation system:
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1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong. Fixed the headers too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:05:51 +00:00
84563b37e5
Partial flattening of the hanger data structure. Hanger data structure is
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not currently as flat as it could / should be, but it's already comparable
to the speed of the reference implementation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3512 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 16:28:49 +00:00
8f9e3e8ad7
Commit for Kiran; but this is now working, barring little exceptions that I've yet to run across...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3511 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 14:21:19 +00:00
6d5556939d
updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version
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to the vlidation directory), using the same md5sum.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 01:47:04 +00:00
c2858c8988
Minor performance enhancement. Checkpoint commit before major performance
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overhaul.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3504 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 21:39:39 +00:00
5ed2818ffb
Forgot to commit code i relied upon
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3503 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 21:01:35 +00:00
736098b58d
A quick commit before running home. This is a re-factored version of the OppositeHomozygoteClassifier which will work with deNovo violations as well. Some code still needs to be migrated from OHC which is wy that walker isn't yet deleted. This'll be up and running tonight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3502 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 20:47:01 +00:00
de134c226d
Removed ability of users to specify annotations to recompute, cleanups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3501 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 19:17:59 +00:00
4d1a6b3d99
quick changes for G
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3500 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 16:33:27 +00:00
907931c902
a) Update annotations when creating new vcf with Beagle's imputed data. Since genotypes may (will) change based on imputation, several annotations need to be updated. By default, AC, AF, AN and AB will be updated. User can force extra annotaqtions to be updated with -A <annotation> argument.
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b) Several cleanups and beautifications.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3499 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 15:12:04 +00:00
aaron
asivache
kshakir
sjia
hanna
weisburd
kiran
ebanks
bthomas
chartl
delangel