b101b9c30b
Add Mongo switch
2012-05-01 14:00:48 -04:00
1b609e9075
Move Mongo to server couchdb
2012-05-01 13:59:47 -04:00
fd57d27f45
Move MongoDB connection handling to a separate class
2012-05-01 13:59:37 -04:00
db3cd1abd5
Use 2 MongoDB collections (tables): one for INFO/attributes, one for samples/genotypes.
2012-05-01 13:57:23 -04:00
04e1be9106
Better handling of Mongo errors + exceptions
2012-05-01 13:57:23 -04:00
ca737479cf
Query for stop locations because we don't have that information in the reference
2012-05-01 13:57:23 -04:00
1cda87a4ad
Set ROD priority list to input
2012-05-01 13:57:23 -04:00
a7fe847faf
Set the priority list and don't bother combining if not needed
2012-05-01 13:57:23 -04:00
f739305f43
Combine the variants found at a location
2012-05-01 13:57:23 -04:00
020f884d5a
Use new key of source ROD plus alleles
2012-05-01 13:57:23 -04:00
221ce9c3d6
Add alleles to the primary key
2012-05-01 13:57:23 -04:00
3198ce5471
Can have multiple variants at a location
2012-05-01 13:57:22 -04:00
11ed8e61c9
Add referenceBaseForIndel to the Mongo VariantContext objects
2012-05-01 13:53:44 -04:00
7ed0ee7ed0
Skip locations with no genotypes instead of throwing a NPE
2012-05-01 13:53:44 -04:00
4bdfeacdaa
Handle multiple samples/genotypes per location
...
TODO: sample selection
2012-05-01 13:53:43 -04:00
1f7c628796
Insert the ROD filename into MongoDB as part of the primary key
2012-05-01 13:53:43 -04:00
bb8a6e9b0a
Initial test of write and read from MongoDB
2012-05-01 13:53:43 -04:00
d93a413f2e
Add MongoDB dependency
2012-05-01 13:53:43 -04:00
0cf3603c73
Merged bug fix from Stable into Unstable
2012-05-01 13:39:27 -04:00
c2b74eca64
Remove unnecessary and obscure usage of old R
2012-05-01 13:39:09 -04:00
c0084c741b
Pilot BCF2 Implementation: Checkpointing the code
...
* Not working yet, still very much a work-in-progress with lots of placeholders
* Needed to check this in to enable possible collaboration, since it's
going slower than anticipated and the conference deadline looms.
2012-05-01 12:23:10 -04:00
fdffe1d61b
Merged bug fix from Stable into Unstable
2012-05-01 11:04:46 -04:00
0c8e801021
Removing public to private dependency
2012-05-01 11:04:11 -04:00
e964d17518
Removing public to private dependency
2012-05-01 11:02:28 -04:00
ef082356e9
Merge remote-tracking branch 'unstable/master'
2012-05-01 08:47:08 -04:00
462450c3e3
disabling all BQSR unit tests
...
with the changes to the cycle covariate, some tests need updates, others need to be completely re-written.
2012-04-30 14:39:55 -04:00
825ad30477
Adding readgroup filter option to BQSR queue script
2012-04-30 14:39:55 -04:00
e185632013
Exhaustive unit tests for Pool SNP genotype likelihoods:
...
a) Add ability for ErrorModel to be specified by external log-probability vector for testing.
b) For a given depth and ploidy(=2*samples/pool), create artificial high quality pileup testing from AC=0 to AC=ploidy, and test that pool GL's have expected content.Misc. refactorings and cleanups
c) Misc. cleanups and beautification.
2012-04-30 14:29:46 -04:00
7d029b9a28
Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-30 12:16:30 -04:00
944a7d815e
Bringing VQSRV3 up to date. Lots of new features (un-classifying the worst-performing training sites, treating the x% best/worst sites as postive/negative points, ability to pass in a monomorphic track to see ROC curves output). Minor changes to AlleleBalance: weighted average was incorrectly specified (using logscale actually biased the average towards the AB of low-quality genotypes), and breaking out AB by het, hom, and diploid to bring it in line with some (private) changes to the indel likelihood model that (correctly) computes these values for indels.
2012-04-28 11:31:03 -04:00
54a9bc2da2
Bug fix in reverse trim alleles for the case of mixed records that become non-mixed after subsetting the alleles.
2012-04-28 09:12:26 -04:00
e332aeaf70
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-27 16:21:21 -04:00
2b5dd28550
Bug fix in reverse trim alleles for the case of mixed records.
2012-04-27 16:21:02 -04:00
c2472b3c45
parallel BQSR implementation.
2012-04-27 15:18:08 -04:00
1db2d1ba82
Do not add the first and last 4 cycles to the recalibration tables.
2012-04-27 15:18:07 -04:00
08dbd756f3
Quick QC walkers to look at the error profile of indels in the read
2012-04-27 15:18:07 -04:00
24173d860a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-27 14:41:38 -04:00
730208133b
Several fixes and improvements to Pool caller with ancillary test functions (not done yet):
...
a) Utility class called Probability Vector that holds a log-probability vector and has the ability to clip ends that deviate largely from max value.
b) Used this class to hold site error model, since likelihoods of error model away from peak are so far down that it's not worth computing with them and just wastes time.
c) Expand unit tests and add an exhaustive test for ErrorModel class.
d) Corrected major math bug in ErrorModel uncovered by exhaustive test: log(e^x) is NOT x if log's base = 10.
e) Refactored utility functions that created artificial pileups for testing into separate class ArtificialPileupTestProvider. Right now functionality is limited (one artificial contig of 10 bp), can only specify pileups in one position with a given number of matches and mismatches to ref) but functionality will be expanded in future to cover more test cases.
f) Use this utility class for IndelGenotypeLikelihoods unit test and for PoolGenotypeLikelihoods unit test (the latter testing functionality still not done).
g) Linearized implementation of biallelic exact model (very simple approach, similar to diploid exact model, just abort if we're past the max value of AC distribution and below a threshold). Still need to add unit tests for this and to expand to multiallelic model.
h) Update integration test md5's due to minor differences stemming from linearized exact model and better error model math
2012-04-27 14:41:17 -04:00
da83076ab5
The name still sounds silly to me, but less silly than before
2012-04-27 14:39:47 -04:00
959f5417f2
Handle complex multi-allelic events
2012-04-27 14:19:41 -04:00
08bebcecbd
Updating the status values
2012-04-27 14:07:48 -04:00
d8f6bc232b
Adding support for non-haplotype-based comparison of multi-allelics (i.e. we do compare alleles and test for partial equality, but we don't construct haplotypes for this yet).
2012-04-27 13:43:52 -04:00
1bbb156afa
Fixing compile error
2012-04-27 12:52:39 -04:00
0439047269
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-27 10:49:45 -04:00
05b44dd017
The genotypeCounts array wasn't always being initialized before it was accessed, leading to a NPE (which got caught and thrown as a JEXL expression when used in selection). Added unit test to cover all genotype count methods.
2012-04-27 10:49:36 -04:00
9801dd114f
Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped
...
The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag()
Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.
2012-04-27 09:58:38 -04:00
005cdcad5b
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-27 09:58:14 -04:00
64077ec7c8
Add option to use XHMM to genotype all possible consecutive sub-segments of CNVs
2012-04-27 01:42:20 -04:00
2ad1aa2a2c
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-26 19:31:47 -04:00
db41d10f54
First (very rough) version of a haplotype-based resolver of alleles from two provided VCF files. It works well on standard cases (e.g. MNP vs. 2 SNPs) but still needs to be tested more thoroughly and I need to add support for multi-allelics (although I know how to do that now). Being committed in private for Ryan's benefit, but no one else should be using it now.
2012-04-26 16:30:22 -04:00
Joel Thibault
Mark DePristo
David Roazen
Eric Banks
Mauricio Carneiro
Guillermo del Angel
Christopher Hartl
Ryan Poplin
Khalid Shakir
Menachem Fromer