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  • 6f095a7752 Merge branch 'laptop' Kiran V Garimella 2011-07-21 03:17:14 -0400
  • c40b0fe1a3 Only evaluate genotypes that have a PQ field Kiran V Garimella 2011-07-21 03:16:57 -0400
  • 11e498979f Merge branch 'laptop' Kiran V Garimella 2011-07-21 03:13:56 -0400
  • 593787c1d0 Only evaluate genotypes that have a PQ field Kiran V Garimella 2011-07-21 03:12:50 -0400
  • f01fc732f4 Merge branch 'laptop' Kiran V Garimella 2011-07-21 03:04:30 -0400
  • 8d7b7e259e Track number of genotypes with PQ field Kiran V Garimella 2011-07-21 03:04:09 -0400
  • d8f5bbeefc Merge branch 'laptop' Kiran V Garimella 2011-07-21 03:02:06 -0400
  • 67031de95c Formatting changes Kiran V Garimella 2011-07-21 03:01:53 -0400
  • c135d8832c Merge branch 'laptop' Kiran V Garimella 2011-07-21 02:59:46 -0400
  • bfecc60fd6 Formatting changes Kiran V Garimella 2011-07-21 02:59:32 -0400
  • a687f04615 Merge branch 'laptop' Kiran V Garimella 2011-07-21 02:51:37 -0400
  • 620a4e5aed Handle missing PQ fields Kiran V Garimella 2011-07-21 02:51:29 -0400
  • 82a0e67219 Merge branch 'laptop' Kiran V Garimella 2011-07-21 02:46:59 -0400
  • c8d381f51e Formatting fixes for haplotype metrics Kiran V Garimella 2011-07-21 02:46:43 -0400
  • 1992973e05 Merge branch 'laptop' Kiran V Garimella 2011-07-21 02:43:19 -0400
  • 3cde209632 Print haplotype metrics Kiran V Garimella 2011-07-21 02:42:58 -0400
  • de239d8f44 Merge branch 'laptop' Kiran V Garimella 2011-07-21 02:16:14 -0400
  • aafe9e6ca7 Try again to suppress hom genotypes Kiran V Garimella 2011-07-21 02:15:44 -0400
  • 77e10a3280 Merge branch 'laptop' Kiran V Garimella 2011-07-21 02:11:02 -0400
  • e5c50fb3de Suppress matching hom genotypes Kiran V Garimella 2011-07-21 02:10:15 -0400
  • 50ab8c513b Merge branch 'laptop' Kiran V Garimella 2011-07-21 02:00:56 -0400
  • ba4b1ce171 Even more formatting changes, trying to get the haplotypes to line up nicely Kiran V Garimella 2011-07-21 02:00:34 -0400
  • 7770ddf2d6 Merge branch 'laptop' Kiran V Garimella 2011-07-21 01:56:44 -0400
  • 5d21f7fa91 Don't show reference allele status Kiran V Garimella 2011-07-21 01:56:39 -0400
  • 7695eb753d More formatting Kiran V Garimella 2011-07-21 01:53:36 -0400
  • 98444cbebb Merge branch 'laptop' Kiran V Garimella 2011-07-21 01:47:01 -0400
  • dcd7d97b60 Formatting. Kiran V Garimella 2011-07-21 01:46:38 -0400
  • e2d0a2c459 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Kiran V Garimella 2011-07-21 01:42:50 -0400
  • 6cf26d8e7f Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/kiran/repositories/Sting-Unstable Kiran V Garimella 2011-07-21 01:40:56 -0400
  • e5b61eb9a0 Walker to compare RBP and Beagle haplotypes Kiran V Garimella 2011-07-21 01:40:25 -0400
  • 6fa17d86ae Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator Mark DePristo 2011-07-21 00:18:07 -0400
  • 32730b1832 Fixed md5 due to new PL ordering Guillermo del Angel 2011-07-20 22:17:15 -0400
  • 45c73ff0e5 Runs and emits an HTML document Mark DePristo 2011-07-20 17:16:33 -0400
  • d31b176e15 Removed GATK use of distributed parallelism framework. Moved distributed GATK prototype code into distributedutils, separating from threading package Mark DePristo 2011-07-20 16:26:09 -0400
  • 4b0b7f4b32 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-20 14:49:25 -0400
  • f14f20d718 Fix bug involving reuse of the sample variable. Cleaned up some otherwise unused comments and code. Matt Hanna 2011-07-20 14:48:33 -0400
  • 0a1d2df8cb Merged bug fix from Stable into Unstable Guillermo del Angel 2011-07-20 13:19:35 -0400
  • f15023b7d2 Bad bug fix: output GLs in multiallelic records were in incorred order (misread spec) Guillermo del Angel 2011-07-20 12:10:48 -0400
  • c09f92ccee Fixing the illegal character accidently entered Mauricio Carneiro 2011-07-20 11:39:04 -0400
  • 4e00666632 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Mauricio Carneiro 2011-07-20 11:38:16 -0400
  • ea90af199c Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Roger Zurawicki 2011-07-20 11:17:36 -0400
  • d3a8363491 Changed MRAV to ADAV Updated ReducedBAMEvaluation to allow multiple parameters to be tested Fixed previous error Roger Zurawicki 2011-07-20 10:49:50 -0400
  • b9c9e0e952 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-07-20 10:45:16 -0400
  • 7140280bf6 Further bug fixes/cleanups for PrintReadsWalker Guillermo del Angel 2011-07-20 10:44:37 -0400
  • a2d90a3590 Bug fix: reverted logic so that default behavior skips over sample lookup Guillermo del Angel 2011-07-20 10:23:10 -0400
  • e8409c80fa Further protection vs null pointers in PrintReadsWalker Guillermo del Angel 2011-07-19 21:59:24 -0400
  • 5d706c9e92 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-07-19 20:25:33 -0400
  • fb2d475c22 Bug fix to prevent null pointer Guillermo del Angel 2011-07-19 20:13:56 -0400
  • 92c7cfa1c8 BWA bindings and tests moved to public (was required for ValidationAmplicons) Christopher Hartl 2011-07-19 20:11:31 -0400
  • baae381acb Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" David Roazen 2011-07-19 18:38:53 -0400
  • eb63b48414 Revert "Resolving conflict" David Roazen 2011-07-19 18:36:53 -0400
  • a3cecf0668 Resolving conflict Roger Zurawicki 2011-07-19 17:20:27 -0400
  • 3d72b98a35 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Roger Zurawicki 2011-07-19 17:16:20 -0400
  • d92d00a85d Changed MRAV to ADAV to reflect real implementation (Max reads to Average Depth at Variant Sites). Optimized Mapping Quality calculation. Correctly filtered reads below minimum Mapping Quality threshold Roger Zurawicki 2011-07-19 16:59:06 -0400
  • 8a7e698883 better debug output for plotting. Mauricio Carneiro 2011-07-19 15:28:54 -0400
  • 07e716d23a PickSequenomProbes2 expanded functionality: lowercasing based on sequence uniqueness, preserving reference base prior to indel (not a part of the VC as I thought it was), masking deletion bases with 'N's, flanking insertion with 'N's, output is a fasta formatted file. Renamed to ValidationAmplicons since this is really not for picking sequenom probes, but for generating amplicon sequence from which other applications (like sequenom) can choose PCR primers. Moved from private to public. Christopher Hartl 2011-07-19 15:21:47 -0400
  • 6181d1e4cb Fixed integration test for VariantsToTable: now the * in REF column is not output Guillermo del Angel 2011-07-19 14:42:11 -0400
  • e6d306458c Merge bug fixes Guillermo del Angel 2011-07-19 14:36:20 -0400
  • 989dd17f95 a) Add ability in PrintReads to specify a sample file to easily subset samples, useful for IGV visualization, b) VariantsToTable is more R-friendly with Indels when printing ref/alt columns, c) Changes to SelectVariants ability to speficy a mask to randomly sample from a given AF distribution Guillermo del Angel 2011-07-19 14:29:07 -0400
  • f7233a5e63 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Kiran V Garimella 2011-07-19 11:13:19 -0400
  • 005adf377f Derive MEDIAN_INSERT_SIZE plot from base plot with additional faceting. Matt Hanna 2011-07-19 10:48:45 -0400
  • 9a1394d7e7 Clean up MEDIAN_INSERT_SIZE plot for consistency with other plots. Matt Hanna 2011-07-19 10:34:50 -0400
  • 5d3112c665 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-19 09:32:01 -0400
  • 0cec2c6759 When sorting samples by date, only use filtered samples to avoid discontinuities in the plot. Add brief documentation for running the R script. Matt Hanna 2011-07-19 09:28:51 -0400
  • 9ad5c7dfa4 Resolving simple conflicts in the data processing pipeline. Mauricio Carneiro 2011-07-19 08:05:11 -0400
  • 7688bda1a6 better progress report for the DPP Mauricio Carneiro 2011-07-18 23:39:47 -0400
  • 2b465ab43b * added optional 'no validation' for the Data Processing pipeline. * some simplifications on the picard classes Mauricio Carneiro 2011-07-18 23:30:31 -0400
  • 4cf7a2af23 Removed broad specific default paths so people from outside the broad can use it. Mauricio Carneiro 2011-07-18 23:25:21 -0400
  • 9b446020f9 Using picard implementations for accessing aggregation directories. Added more utilities to PicardPrivate. Revved picard. Khalid Shakir 2011-07-18 21:49:03 -0400
  • 0ef37979cc Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-18 21:30:51 -0400
  • d5d107856c Subselect based on bait set. Matt Hanna 2011-07-18 18:42:21 -0400
  • 1837da37f6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Mauricio Carneiro 2011-07-18 17:59:26 -0400
  • 916c0c9489 some quick & dirty debug info for the replication validation walker. Mauricio Carneiro 2011-07-18 17:57:12 -0400
  • 044f5faa4d Support for numeric columns. Matt Hanna 2011-07-18 17:44:49 -0400
  • 9729d61e2d Use geom_text() instead of geom_point() when outputting data for new project only. Matt Hanna 2011-07-18 17:29:00 -0400
  • f1e3c3356b Merge branch 'rbam' Mauricio Carneiro 2011-07-18 17:26:07 -0400
  • c618a5b54c commented out wrong MD5s Mauricio Carneiro 2011-07-18 17:25:45 -0400
  • a9f956c80c Fixed several bugs in the pooled caller. Creating a good dataset to test its accuracy now. Mauricio Carneiro 2011-07-18 16:04:11 -0400
  • 4e78f0b064 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-07-18 15:45:23 -0400
  • 8f0badc52b Updating md5s, as the diffobjects walker now emits the summary in reverse order. Mark DePristo 2011-07-18 15:44:21 -0400
  • c05451047c Support for multiple records at the same site. The first record gets chr:start, and subsequent records get chr:start_2, chr:start_3, etc. Mark DePristo 2011-07-18 15:43:52 -0400
  • 782a05e9b5 Support for sorting the diff output in reverse order. Mark DePristo 2011-07-18 15:43:01 -0400
  • 45702d3084 Now supports a mode where the primary key isn't sorted. In this case the records are displayed in the order in which they are added to to the table. Mark DePristo 2011-07-18 15:40:15 -0400
  • 15b44ac2c3 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-18 14:56:41 -0400
  • e5e7523f8b Modify to support either bam list format files or tsv formatted files. The latter provide a major advantage when dealing with samples with spaces in the names. Matt Hanna 2011-07-18 14:56:00 -0400
  • 9eb83bed64 Percentages should be represented as percentages and not, you know, something else. Kiran V Garimella 2011-07-18 14:40:38 -0400
  • adce37774a Add functionality for tsv output. Matt Hanna 2011-07-18 14:12:01 -0400
  • 6d5e87da10 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-07-18 13:59:10 -0400
  • 83ba2c066a Making it deterministic Eric Banks 2011-07-18 13:59:02 -0400
  • 92fa410450 Check that it's a valid bam file before parsing or bad things can happen Eric Banks 2011-07-18 13:43:34 -0400
  • 80b5c5261a CombineVariants no longer combines records of different types. So now when combining SNP and indel callsets, overlapping calls get their own records. Useful for Khalid in the pipeline. For those interested, it turns out the previous behavior was doing the wrong thing occasionally (and this was even captured in the integration tests). Eric Banks 2011-07-18 13:42:45 -0400
  • 4adead3099 Fixed import conflict Menachem Fromer 2011-07-18 13:23:20 -0400
  • d8ba4ab835 Only maintain an unbroken haplotype chain if the current is phased relative to previous (by RBP), or both previous and current are parentally phased Menachem Fromer 2011-07-18 13:14:39 -0400
  • d05d79218b Implemented minimum quality equivalent argument Mapping quality now takes a root mean square (slow) Implemented Quality Equivalent (QE=i) (1 to 64) Roger Zurawicki 2011-07-18 13:08:22 -0400
  • bc8b5da698 Added docs while I was reading through the code to understand it Eric Banks 2011-07-18 12:25:54 -0400
  • 5493a4dd99 Added annotations to filter out : * unmapped reads * failed vendor quality reads * duplicate reads * not primary alignment reads Mauricio Carneiro 2011-07-18 12:06:08 -0400
  • d8517a000a Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-18 11:07:18 -0400
  • f15357c2e1 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-18 10:52:31 -0400
  • 95c776bf59 Updated documentation. Matt Hanna 2011-07-18 10:52:06 -0400
  • cb9bef6847 Updated documentation. Matt Hanna 2011-07-18 10:51:22 -0400