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6577 Commits (504b3ef5ef32eb2c7ed10b9d8e355c59fa6b0017)

Author SHA1 Message Date
Kiran V Garimella 504b3ef5ef Removed constraint to only evaluate eval and comp tracks at sites where genotypes match. 2011-07-25 14:58:10 -04:00
Kiran V Garimella a2d280b85e Forgot to change the name of the switchState columns 2011-07-25 14:06:41 -04:00
Kiran V Garimella a0dd166364 Print metrics for both the unphased and rbp-phased data for easier comparison. 2011-07-25 13:53:33 -04:00
Kiran V Garimella 62011403b0 Constrains evaluation to places where both the unphased and rbp-phased data show the same genotype. 2011-07-25 13:00:29 -04:00
Kiran V Garimella 0eecda6be4 Forgot to toggle switch state when genotypes are first seen in a reversed or consistent phase. 2011-07-25 11:50:02 -04:00
Kiran V Garimella 6389b29c4f Computes the switch error rate for many samples at a time. 2011-07-25 11:36:08 -04:00
Kiran V Garimella 0b43ee117c Added the required=false tag to the -noST and -noEV arguments so the auto-help output doesn't look weird (i.e. listing arguments as required when their value has already been specified by default). 2011-07-25 11:35:34 -04:00
Kiran V Garimella 0b36b6540f Merge branch 'laptop' 2011-07-23 01:44:54 -04:00
Kiran V Garimella e23cb27451 Modified MD5 to account for the triple hets that shouldn't be phased 2011-07-23 01:44:44 -04:00
Kiran V Garimella 1dba8b768c Merge branch 'laptop' 2011-07-23 01:39:15 -04:00
Kiran V Garimella 57e3d136eb Don't try to phase triple-hets either. 2011-07-23 01:38:58 -04:00
Kiran V Garimella f366124778 Merge branch 'laptop' 2011-07-23 01:25:36 -04:00
Kiran V Garimella 45f2ca8d99 Changed MD5 to reflect latest changes to PhaseByTransmission. 2011-07-23 01:21:07 -04:00
Kiran V Garimella 5af9d50183 Merge branch 'laptop' 2011-07-23 01:12:06 -04:00
Kiran V Garimella 5521919cc9 Fixed bug where variants to phase were not being selected properly. 2011-07-23 01:11:28 -04:00
Kiran V Garimella 7da99388ac Merge branch 'laptop' 2011-07-23 01:01:11 -04:00
Kiran V Garimella 58eed20b83 Copy all entries from the attributes map, rather than attempting to modify an unmodifiable map. 2011-07-23 01:00:46 -04:00
Kiran V Garimella b5deff48e6 Merge branch 'laptop' 2011-07-23 00:56:50 -04:00
Kiran V Garimella 5638017137 Removed the nofilters argument specification in the integrationtest 2011-07-23 00:56:23 -04:00
Kiran V Garimella ffa361f57f Merge branch 'laptop' 2011-07-23 00:50:38 -04:00
Kiran V Garimella 9417ba8c2c Modified to accept multi-sample VCFs, removed the application of filters, and changed transmission probability field to be a genotype field rather than an INFO field. 2011-07-23 00:48:26 -04:00
Kiran V Garimella 051c1dc639 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-22 15:59:00 -04:00
Eric Banks d7b3f40259 Merge remote-tracking branch 'unstable/master' 2011-07-22 14:45:24 -04:00
Mauricio Carneiro 4f78025b0b Merged bug fix from Stable into Unstable 2011-07-22 14:42:04 -04:00
Mauricio Carneiro 4080e2cd88 * Added the decoy reference to the bundle under the b37 resources. 
* Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki).
 2011-07-22 14:41:22 -04:00
Matt Hanna f50145b872 Reinitialize random seed in the bwa bindings from the fixed seed stored in the 
BWA support files every time the support files are loaded.
 2011-07-22 13:41:53 -04:00
Kiran V Garimella b8a0fd2a8d Multiply fractionRandom by 100.0 so that the line that indicates the percentage of variants that will be output says (for instance) 90%, not 0.9% 2011-07-22 11:54:59 -04:00
Guillermo del Angel 3d0853149b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-22 08:13:58 -04:00
Guillermo del Angel 6afe63690d Two more true oneoffs (committed mostly for didactic purposes): codec that reads Mills/Devine indel table into a vcf and another (in progress) that will read indel chip genotype data and produce a vcf 2011-07-22 08:13:05 -04:00
Khalid Shakir 8b8f121cfb Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-21 23:01:11 -04:00
Khalid Shakir 59eb1f4663 Memory limits changed from Int to Double. 
Updated LSF calls to read memory units from config along with tweaks to select hosts.
Moved some common code from GridEngine and LSF to super classes.
 2011-07-21 22:57:18 -04:00
Guillermo del Angel 87f991aee7 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-21 13:35:24 -04:00
Christopher Hartl 2f5d10d16b Fix bug wherein aligner could be closed prior to its being used to lowercase sequences. 2011-07-21 13:21:48 -04:00
Matt Hanna 7054c5342f When using the BWA bindings, you have to explicitly call close() to get the 
bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
 2011-07-21 12:13:29 -04:00
Guillermo del Angel 84c66d4b92 Bug fixes 2011-07-21 11:52:51 -04:00
Guillermo del Angel c4684f4659 A true oneoff: walker that reads in vcf with multiallelic PL's in wrong ordering and flips them around to output in correct order 2011-07-21 11:20:46 -04:00
Kiran V Garimella 623143454b Merge branch 'laptop' 2011-07-21 11:07:02 -04:00
Kiran V Garimella bf6388fa8c Print haplotype start locus 2011-07-21 11:06:45 -04:00
Christopher Hartl 15610ce0c3 Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage. 2011-07-21 11:04:22 -04:00
Kiran V Garimella 1aefc02d2e Merge branch 'laptop' 2011-07-21 10:54:15 -04:00
Kiran V Garimella 45e536dca8 Reenable haplotype printing 2011-07-21 10:40:40 -04:00
Guillermo del Angel 664246937c Try to resolve merge conflict 2011-07-21 10:19:26 -04:00
Kiran V Garimella 1933be36b4 Ignore sites where the alleles don't match between the two files 2011-07-21 03:44:02 -04:00
Kiran V Garimella d9909537ef Merge branch 'laptop' 2011-07-21 03:22:59 -04:00
Kiran V Garimella 58873c391f Don't print the haplotypes anymore - the metrics will do 2011-07-21 03:22:44 -04:00
Kiran V Garimella 6f095a7752 Merge branch 'laptop' 2011-07-21 03:17:14 -04:00
Kiran V Garimella c40b0fe1a3 Only evaluate genotypes that have a PQ field 2011-07-21 03:16:57 -04:00
Kiran V Garimella 11e498979f Merge branch 'laptop' 2011-07-21 03:13:56 -04:00
Kiran V Garimella 593787c1d0 Only evaluate genotypes that have a PQ field 2011-07-21 03:12:50 -04:00
Kiran V Garimella f01fc732f4 Merge branch 'laptop' 2011-07-21 03:04:30 -04:00