7aa030a9a4
Hmm. Apparently variants can get lifted over to different chromosomes. Who knew? Reverting changes from a couple of days ago. The only way to do this correctly (without requiring lots of memory) is to turn off on-the-fly indexing for this walker. Integration tests cover this now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4510 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-17 02:54:12 +00:00
196029c0b4
Removed obsolete -bsubWait from sanity check.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4509 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-16 02:14:34 +00:00
9dc2e931b6
Saving the order functions are added to in the QScript. Using the order during submission of ready jobs (but not currently dryrun) and during -status.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4508 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 20:00:35 +00:00
8b2d387643
Added in an eval module that calculates the dispersion histograms between eval and comp (e.g. M_{i,j} = # of times eval observed to have AC i, comp AC j -- for af it's i/100 vs j/100 )
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4507 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 19:07:43 +00:00
f78ff08e2b
This is less correct than my previous change but it's what UGv1 does and now is not the right time to start mucking with things.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4506 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 18:56:45 +00:00
471c18054f
Fix for SB calculation: the best overall AF might not have any mass when just looking at reads from a single strand. We need to compute the best AF for each stratification.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4505 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 17:51:18 +00:00
7157cb9090
While bkill'ing on the shutdown thread Queue will no longer try to submit more jobs on the original thread.
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Updated pipeline output structure to current recommendations by Corin.
Directories are now automatically before the function runs.
Fixed several bugs with scatter gather binding when the script author needs to change the directories.
Fixed bug with tracking of log files for CloneFunctions.
More error handling and logging of exceptions (good test environment while LSF was down this early AM!)
Removed cleanup utility for scatter gather. SG Output structure has changed significantly. Will need to discuss and find a better approach for Queue programatically deleting files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4504 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 17:01:36 +00:00
42c3d74432
bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4503 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 16:27:40 +00:00
c9d473edee
More changes to Variant Eval and Genotype Concordance (passes all integration tests):
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1: -sample can now include a file, which will be parsed for sample-name entries
2: If you request a sample to run analysis on, but it is not present in any of your RODs, VEW will exception out
3: Change added to parse Integer, String, and List<Integer> type Allele Count annotations (error otherwise)
4 [slightly problematic]: The count objects now maintain row-keys in order, as the keys were taking an inordinate amount of time in onTraversalDone (multiple calls to getRowKeys(), so many multiple sorts of the same underlying unsorted object, very bad)
There is a legacy comparison object which is unused which I will strip out soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4502 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 12:40:36 +00:00
3d988576a6
updated liftover script: it no longer needs to re-sort the vcf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4501 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 08:03:41 +00:00
954dd84f51
Adding an integration test (against hg18 this time) that requires on-the-fly sorting in order to work properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4500 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 07:45:21 +00:00
9f54170dff
Hooking up the liftover tool to the new on-the-fly sorting VCF writer so that records can now get emitted in order.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4499 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 07:27:01 +00:00
d41c252b13
Looking over the calling results with Ryan, it's clear that while the grid search optimization (ignoring samples that are clearly ref) can work for assigning genotypes, it cannot be used for calculating P(AF>0). There's too much area under the likelihood curve that gets lost and the QUALs are negatively affected. However, testing showed that this only slightly affects runtime (~15 minutes per 1Mbase for the 1kg allpops). The optimization does remain for genotyping.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4498 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 19:06:32 +00:00
5e0c4ecc21
Added DbSnp to VariantEval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4497 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 17:02:17 +00:00
63e3848187
Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4496 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 15:58:52 +00:00
2606e67cf1
Reverting Matt's change from yesterday which I accidentally blew away when trying to cope with the stupid svn update issues we've been plagued with recently.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4495 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 14:40:42 +00:00
cfb33d8e12
Filtering optimizations are now live for UGv2. Instead of re-computing filtered bases at every locus, they are computed just once per read and stored in the read itself. Eyeballing the results on the ~600 sample set from 1kg, we cut out ~40% of the runtime! QUALs are now sometimes different from UGv1 because I noticed a bug in v1 where samples with spanning deletions only were assigned ref calls instead of no-calls which ever so slightly affects the QUAL. Not a big deal though.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4494 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 05:04:28 +00:00
4ac636e288
Minor change: when tabulating concordance by AC, ignore sites with multiple segregating alleles in the population, at least for now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4493 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 01:35:33 +00:00
5034ca18dc
...and forgot to sync up the changes to CommandLineFunction with CloneFunction.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4492 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 22:40:02 +00:00
7c9ef59d65
This is simultaneously a minor and major change to VariantEval, so take heed:
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The core walker has been modified so that when variant contexts (eval and comp) are subset to command-line-specified sample(s), the chromosome count annotations (AC/AN/AF) are altered to reflect the AC/AN/AF of only those samples involved in the comparison. No more getting AC500 when you're comparing a 10-sample overlap. Interestingly enough, this didn't break any integration tests.
GenotypeConcordance now has two additional tables: Allele Count Statistics, and Allele Count Summary Statistics. These work exactly identically to the Sample Statistics and Sample Summary Statistics tables, except that the partition being used is no longer the sample, but instead the allele count of the variant sites. These tables stratify by both eval and comp ACs, e.g.
evalAC0
evalAC1
evalAC2
compAC0
compAC1
compAC2
Differences with previous integration tests were verified to only be in the Allele Count tables (by grepping them out of the diff); a new test has been added for the simple case of an AC=1 site in the eval becoming an AC=2 site in the comp.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4491 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 22:26:15 +00:00
5ee12875fb
Emergency fix for Ryan:
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- Catching errors when LSF fails and retrying.
- When LSF retries fail, catching the error, marking the job as failed, and no longer bkilling everything by exiting Queue.
- Caching function fields by class instead of each instance of a function saving a list of its fields.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4490 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 22:22:01 +00:00
83b8676b69
Hack to fix mysterious disappearing read attributes. Ultimately caused
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by the fact that the GATKSAMRecord, by design, needs to both inherit from
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.
Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation. But in
the short-term, there's no obvious fix.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 19:06:54 +00:00
da29fcdb68
No longer writes the index to disk twice. But fixes for closing VCFWriters throughout the codebase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4488 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 14:26:06 +00:00
28a1020c89
comment out debugging line that was clogging the performance test output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4487 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 03:26:55 +00:00
272ac2ae4a
more fixes for tests broken by indexing-on-the-fly; I think this should do it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4486 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 01:54:32 +00:00
ed39af53cd
Fix for exception when trying to load reference segment for a read that aligns
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to 0 bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4485 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 23:50:51 +00:00
fe9f128631
Better fix for earlier bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4484 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 19:21:33 +00:00
ff0df1a2da
A fix for an integration test that was broken by on-the-fly indexing. Also, better reporting of Tribble exceptions in GATK integration tests. Trying to get the tests back up and running...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4483 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 18:39:56 +00:00
69652e08c6
Bug fix for reads that completely fall within an insertion: the I cigar string element was 1 base too long.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4482 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 14:46:21 +00:00
f348ca2976
Now processes VCF files with repeated loci without crashing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4481 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 04:36:07 +00:00
ccc22c2331
Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4480 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 01:40:43 +00:00
f5b66647ac
Include all standard annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4479 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-11 20:52:08 +00:00
fd8351cd49
Get rid of useless test/'optimization' that was carried over from UGv1. New codde is (minimally) faster with same results.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4478 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-11 04:04:07 +00:00
f28523e7de
Implemented SB for UGv2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4477 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-11 03:56:01 +00:00
7008a469dc
Update MalformedReadFilter to pass reads that have cigar strings like 40S36I
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that have 0 aligned bases in the genome. We'll have to fix walkers as faults
appear.
Also added JIRA GSA-406: finer-grained control of MalformedReadFilter: want
to exception out by default in these cases but pass them with a warning with
a corresponding -U flag.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4476 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-11 03:01:04 +00:00
530875817f
Experimental code for better filtering of bases in sam records. Not hooked up yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4475 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-11 02:19:51 +00:00
a0de269c4b
Better message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4474 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-10 20:11:51 +00:00
0a4cf02a52
Fix for index out of bounds exception in VR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4473 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-10 17:35:15 +00:00
116309b3c3
More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4472 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 20:22:12 +00:00
38a67fed63
High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4471 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 19:53:21 +00:00
6368a46bab
Scala protected is more akin to Java private than Java protected. Not typing these defs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4470 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 19:36:23 +00:00
bdd3a9752e
Changed min MQ and BQ to 20 (for phasing)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4469 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 19:27:45 +00:00
05500d1a8d
An iterator wrapper/adapter: takes GenomeLoc iterators 1 and 2 and traverses intersections of intervals from 1 with intervals from 2. Both 1 and 2 must be SORTED and NON_OVERLAPPING, but this iterator does NOT perfrom any checks, so if these conditions are not met, the behavior is unspecified
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4468 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 16:34:00 +00:00
253d528e49
not ready for commit yet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4467 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 15:30:55 +00:00
4f2f33b42a
fix method invocation to conform to new API; this version of the code will compile but new functionality is still not fully in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4466 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 15:30:26 +00:00
cece19d4d2
not ready for commit yet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4465 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 15:14:54 +00:00
39e373af6e
deleting accidentally committed junk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4464 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 15:13:01 +00:00
b3d81984aa
renaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4462 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 14:10:11 +00:00
77dddd0afa
renaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4461 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 14:08:28 +00:00
bffb8bb01f
The SVN repository is not for dumb analysis-specific scripts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4460 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 14:04:53 +00:00
ebanks
kshakir
chartl
asivache
corin
hanna
depristo
aaron
kiran
rpoplin
fromer