dce2c17404
Added "-bsubWait" where Queue waits for all the jobs to exit before exiting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3661 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 19:52:17 +00:00
20f5fdbcf7
Changes to MVC to make the the header of its output VCF compliant with spec (give expected # of values for info field annotations)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3660 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 18:33:23 +00:00
c047232b18
Using picard for bam merging.
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Properties now propagate to scatter/gather functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3659 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 17:59:09 +00:00
62d22ff1aa
adding the original allele list to a variant context (as the annotation ORIGINAL_ALLELE_LIST), in the case where the set alleles are the result of clipping. Added tests for both cases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3658 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 17:23:46 +00:00
1292c96e29
The cleaner now adds the OC (original cigar) and OS (original alignment start) tags as appropriate to reads that get realigned; this feature can be turned off. Also, improved integration tests (sorry, Kiran!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3657 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 16:46:47 +00:00
cc8d8eaedb
Now that we always reserve space for two read ends when collecting stats stratified by libraries, we need to check that the second end was indeed present; otherwise the pointer is null and this was causing an exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3656 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 16:40:16 +00:00
26ef1f84bf
Updates to not depend on an environment variable to figure out where libraries are (helpful for installation at the Sanger).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3655 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 15:46:41 +00:00
9a24598a98
By default, don't clean reads with mates mapped to other chromosomes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3654 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 15:14:20 +00:00
e7939f7036
Fixed error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3653 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 14:50:28 +00:00
b2127e59c4
A first draft of scripts and LaTeX templates required to automatically generate slides for the 1,000 Genomes Automated Data Processing Report.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3652 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 14:30:50 +00:00
bf5cbad04c
Make the target creator a rod walker (that allows reads) so that we can easily trigger the cleaner on only known indel sites. Adding an integration test to cover this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3651 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 13:28:37 +00:00
464ac63a22
Allowing N's in ALT field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3650 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 11:41:32 +00:00
3a9d426ca8
Added hasPileupBeenDownsampled() boolean to ReadBackedPileup, so that a pileup can report whether or not (but not how much) it's been downsampled.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3649 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 04:56:33 +00:00
8e848ccd84
SAMFileWriters can now write to /dev/null without throwing exceptions, so we can remove the try/catch blocks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3648 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-27 03:59:10 +00:00
09ccdf83b2
fixing a broken test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3647 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 21:59:00 +00:00
d6cbe4d0ad
Bug fixes to support haploid genotypes, optimization for indexing, now tracks the line of the VCF and catches errors to tell you the line no and line when a parsing error occurred.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3646 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 21:08:41 +00:00
5f8a3f95ef
The GT field once again reigns supreme (it must be the first genotype field). Thanks for the catch Eric.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3645 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 21:03:05 +00:00
894ad354fa
Fixed typo in the name of the shell directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3644 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 20:59:40 +00:00
75c98c42b8
Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input.
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Checked in example qscripts that are basically todo integration tests.
Replaced use of queue @Input/@Output with Sting's new @Input/@Output. This means you'll now have to doc-ument the annotations.
More work on dependency resolution cycles being created in the graph during scatter/gather.
Filtering nulls to avoid NPE exceptions in scala's 'Collection'.hashCode.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3643 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 20:51:13 +00:00
147ba68441
Fixed bug with mrnaCoord field - made it count exon positions only, rather than introns & exons
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3642 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 19:53:32 +00:00
ce27ed0d60
Added missing @ClassType to memory limits.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3641 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 18:56:35 +00:00
dff4c06763
Rev'ing Tribble with a special version that has excluded VCF 3.3
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3640 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 18:20:51 +00:00
d3848745ab
moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3639 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 18:20:06 +00:00
b3edb7dc08
two fixes for the VCF 4 parser:
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- Allow the "GT" field in genotypes at any point in the genotype string (before we required they be the first key-value pair).
- Fix a bug with the phasing value put into the VariantContext, thanks for the catch Guillermo!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3638 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 18:01:23 +00:00
e15fe6858e
Disabling test - Will need to update big-tables soon.. will re-enable after updating md5
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3637 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 15:43:41 +00:00
efa60e5de5
and add changes to the vcf used in testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3636 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 02:56:02 +00:00
f9c7803d4e
this got left off my last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3635 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 02:42:44 +00:00
1cb8f51f8c
Fixed -t arg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3634 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 23:44:10 +00:00
3cd0570c1e
Now can run with multiple processes, multiple threads, or both
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3633 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 23:25:01 +00:00
dae3ce2c0f
changed log dir
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3632 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 23:08:13 +00:00
fea8054e9e
Updated long name for -l to --run-locally
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3631 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 22:26:45 +00:00
682f9b46c6
Two fixes together:
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1) Some improvements to the VCF4 parsing, including disabling validation.
2) Reimplemented RefSeq in the new Tribble-style rod system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3630 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 22:17:03 +00:00
72e669538e
Updated arg description for -s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3629 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 22:04:01 +00:00
62bc7651a8
fix for PSPW with DbSNP mask. Added an integration test for this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3628 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 19:31:32 +00:00
4840ef6d3e
Another rev of picard for /dev/null writing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3627 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 19:22:47 +00:00
c32f9d78ae
Rev picard again, this time for error writing to /dev/null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3626 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 04:08:26 +00:00
bcab0eba01
This replaces tearsheet.r, neatens up graphics, and allows the script to be used in R's interactive environment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3625 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 01:02:58 +00:00
8a9b2f4256
removing the GLF ROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3624 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 22:51:45 +00:00
17d2043354
bug fix: now contigs not present in the sequence dictionary are registered properly and do not cause the script to break
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3623 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 20:59:38 +00:00
611d834092
a couple of VCF 4 improvements:
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-Validation of INFO and FORMAT fields.
-Conversion to the the correct type for info fields (i.e. allele frequency is now stored as a float instead of a string).
-Checks for CNV style alternate allele encodings( i.e. <INS:ME:L1>), right now we exception out. Maybe we should just warn the user?
-Tests for the multiple-base polymorphism allele case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3622 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 20:21:43 +00:00
54ae0b8e4e
some updates to tribble for the svn commit that will follow
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3621 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 20:20:07 +00:00
f0fc34bb8e
Bug fix: N's are allowed in the ref so don't fail when e.g. dbsnp has an N!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3620 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 17:49:14 +00:00
b6bceb39b0
Fixing up output for performance tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3619 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 17:00:17 +00:00
75d4736600
Committing changes to comp overlap for indels. Passes all integration tests; minor changes to MVC walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3618 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 15:49:13 +00:00
9b8775180e
Turn on the memory improvement by default (assume the target interval list is sorted, since it is 99.9% of the time). Make the user throw a flag when it's specfically not sorted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3617 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 15:44:55 +00:00
26d51bbe14
Another round of optimizations from Alec. Switching the header merger to
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an IdentityHashMap provides another 10x+ performance boost over his previous
optimization for us.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3616 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 14:54:58 +00:00
003dd4de3e
Rev Picard with performance enhancements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 22:54:23 +00:00
0cafd3d642
clip VCF alleles for indels: only a single left base, and as many right bases as align before converting to variant context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3614 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 22:42:38 +00:00
9872b65803
clip to the null allele on the reference string in VCF 4, instead of stopping to perserve one reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3613 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 20:52:19 +00:00
b5df2705c9
-Remove Nway output option
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-Remove in-memory sorting
-Default to name-sorting (although we allow coordinate sorting with the --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe flag).
Cleaner, faster code. Wiki has been updated (including how to use FixMateInformation.jar from Picard). More changes coming soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3612 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 20:31:55 +00:00
kshakir
chartl
aaron
ebanks
asivache
kiran
weisburd
hanna
depristo
corin