804facb0cc
Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?!
...
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
c0370f4d0a
Added both inclusive and exclusive filters
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3538 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 18:40:41 +00:00
e6d8faf293
making 'parseLocation' public static - as simple as the logic is, it's better kept in one place and I need it!
...
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).
...
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
dde93e743f
always output a brief test summary to the screen, and xml to disk
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3535 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 16:24:50 +00:00
22620ba95c
Adding "abi_solid" to the list of known platforms.
...
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:
...
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.
...
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
d1a4c4f0d3
Added -w filter option allowing user to specify chromosomes to be skipped.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3531 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:58:25 +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(..).
...
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
...
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
e27951ab39
re-updating the VCF code to handle spaces in sample names
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3528 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:18:34 +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
...
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.
...
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.
...
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.
...
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.
...
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(..)
...
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.
...
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
...
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
...
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).
...
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
...
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
...
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
6fd2d39a7d
Modified run_locally mode to use os.system(..) instead of popen
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3515 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:10:03 +00:00
a3ccf49f5b
Write error to stderr
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3514 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:09:10 +00:00
9b2fcc4711
Refactoring of the annotation system:
...
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
...
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...
...
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
6febd0291d
rev tribble to include some dbsnp clean-up and fixes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3510 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 03:08:31 +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
...
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
2b31975cb4
Added more options for coordinate systems - now you can add 1 to either the start coordinates, the end coordinates, or both
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3508 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:49:19 +00:00
410afcdf2c
Added parallelization options - when running locally, multiple processes can be spawned, or a -nt arg can be specified to run each TranscriptToInfo instance multi-threaded
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3507 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:48:07 +00:00
92c72d3361
Added back lines that update the *big-table-header.txt file before using it
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3506 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:45:41 +00:00
3c24223d02
Script for concatenating 2 AnnotatorInputTables, and writing the result to standard out. Merge-sorts the 2 tables while concatenating them
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3505 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:44:16 +00:00
c2858c8988
Minor performance enhancement. Checkpoint commit before major performance
...
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
...
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.
...
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.
...
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
...
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.
...
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
933133ee28
Initial commit of the opposite homozygote classifier. Currently does the following, given a trio vcf:
...
+ Identifies opposite homozygote sites
+ Identifies the parent from whom it is expected that a null allele was inherited (or whether it was a putative genotype error; e.g. mom=homref, dad=homref, child=homvar)
+ Labels each opposite homozygote with its homozygous region in the child (e.g. region 1, region 2)
+ Labels each opposite homozygote with the size of the homozygous region in which it was found, the number of child homozygotes in the region, and the number of opposite homozygote violations within that region
To come:
+ Classification of sites as likely tri-allelic
Note that this is very experimental
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3498 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 03:56:07 +00:00
199e4208cd
Bug fixes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3497 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 00:30:33 +00:00
52ab9f2417
Feature parity between LocusIteratorByState, DownsamplingLocusIteratorByState, including pushing mrl /
...
the LocusOverflowTracker into LocusIteratorByState. Note that the 'Matt Hanna exception', is still enabled
because I haven't yet validated the performance of the DownsamplingLocusIteratorByState when running
without downsampling.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3496 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 22:58:21 +00:00
5c4d070566
Push Mark's changes in LocusIteratorByState into DownsamplingLocusIteratorByState
...
in preparation for merging the two into one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3495 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 17:29:30 +00:00
6eeb1693ca
JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 00:33:02 +00:00
c1ecf75dd5
Update to the latest rev of the picard sharding patch. Includes updates reflecting
...
the imminent move of IlluminaUtil into picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 20:33:21 +00:00
c503f01dcf
More cleanup
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3492 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 17:41:38 +00:00
d4c66d6191
a) Small cleanup
...
b) Fix major issue with Beagle likelihood converter: if likelihood triplets from UG end up being too low, then Beagle input file will be produced with 0.00,0.00,0.00 triplet. If all samples at a marker have this issue, Beagle will effectively produce junk. To fix, likelihoods are renormalized before converting to linear space.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3491 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 17:31:59 +00:00
cfa18f6743
Fixing missed update with new Allele in it
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3490 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 23:56:34 +00:00
kiran
weisburd
asivache
ebanks
aaron
bthomas
hanna
chartl
delangel
depristo