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6465 Commits (1933be36b45cf101dcd60da5809cba7ec7d18281)

Author SHA1 Message Date
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 58873c391f Don't print the haplotypes anymore - the metrics will do 2011-07-21 03:22:44 -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 593787c1d0 Only evaluate genotypes that have a PQ field 2011-07-21 03:12:50 -04:00
Kiran V Garimella 8d7b7e259e Track number of genotypes with PQ field 2011-07-21 03:04:09 -04:00
Kiran V Garimella 67031de95c Formatting changes 2011-07-21 03:01:53 -04:00
Kiran V Garimella bfecc60fd6 Formatting changes 2011-07-21 02:59:32 -04:00
Kiran V Garimella 620a4e5aed Handle missing PQ fields 2011-07-21 02:51:29 -04:00
Kiran V Garimella c8d381f51e Formatting fixes for haplotype metrics 2011-07-21 02:46:43 -04:00
Kiran V Garimella 3cde209632 Print haplotype metrics 2011-07-21 02:42:58 -04:00
Kiran V Garimella aafe9e6ca7 Try again to suppress hom genotypes 2011-07-21 02:15:44 -04:00
Kiran V Garimella e5c50fb3de Suppress matching hom genotypes 2011-07-21 02:10:15 -04:00
Kiran V Garimella ba4b1ce171 Even more formatting changes, trying to get the haplotypes to line up nicely 2011-07-21 02:00:34 -04:00
Kiran V Garimella 5d21f7fa91 Don't show reference allele status 2011-07-21 01:56:39 -04:00
Kiran V Garimella 7695eb753d More formatting 2011-07-21 01:53:36 -04:00
Kiran V Garimella dcd7d97b60 Formatting. 2011-07-21 01:46:38 -04:00
Kiran V Garimella 6cf26d8e7f Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/kiran/repositories/Sting-Unstable 2011-07-21 01:40:56 -04:00
Kiran V Garimella e5b61eb9a0 Walker to compare RBP and Beagle haplotypes 2011-07-21 01:40:25 -04:00
Kiran V Garimella f7233a5e63 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-19 11:13:19 -04:00
Matt Hanna 005adf377f Derive MEDIAN_INSERT_SIZE plot from base plot with additional faceting. 2011-07-19 10:48:45 -04:00
Matt Hanna 9a1394d7e7 Clean up MEDIAN_INSERT_SIZE plot for consistency with other plots. 2011-07-19 10:34:50 -04:00
Matt Hanna 5d3112c665 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-19 09:32:01 -04:00
Matt Hanna 0cec2c6759 When sorting samples by date, only use filtered samples to avoid discontinuities 
in the plot.  Add brief documentation for running the R script.
 2011-07-19 09:28:51 -04:00
Mauricio Carneiro 9ad5c7dfa4 Resolving simple conflicts in the data processing pipeline. 
Conflicts:
	public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
 2011-07-19 08:05:11 -04:00
Mauricio Carneiro 7688bda1a6 better progress report for the DPP 2011-07-18 23:39:47 -04:00
Mauricio Carneiro 2b465ab43b * added optional 'no validation' for the Data Processing pipeline. 
* some simplifications on the picard classes
 2011-07-18 23:30:31 -04:00
Mauricio Carneiro 4cf7a2af23 Removed broad specific default paths so people from outside the broad can use it. 2011-07-18 23:25:21 -04:00
Khalid Shakir 9b446020f9 Using picard implementations for accessing aggregation directories. 
Added more utilities to PicardPrivate.
Revved picard.
 2011-07-18 21:49:03 -04:00
Matt Hanna 0ef37979cc Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 21:30:51 -04:00
Matt Hanna d5d107856c Subselect based on bait set. 2011-07-18 18:42:21 -04:00
Mauricio Carneiro 1837da37f6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 17:59:26 -04:00
Mauricio Carneiro 916c0c9489 some quick & dirty debug info for the replication validation walker. 2011-07-18 17:57:12 -04:00
Matt Hanna 044f5faa4d Support for numeric columns. 2011-07-18 17:44:49 -04:00
Matt Hanna 9729d61e2d Use geom_text() instead of geom_point() when outputting data for new project 
only.
 2011-07-18 17:29:00 -04:00
Mauricio Carneiro f1e3c3356b Merge branch 'rbam' 2011-07-18 17:26:07 -04:00
Mauricio Carneiro c618a5b54c commented out wrong MD5s 2011-07-18 17:25:45 -04:00
Mauricio Carneiro a9f956c80c Fixed several bugs in the pooled caller. Creating a good dataset to test its accuracy now. 2011-07-18 16:04:11 -04:00
Mark DePristo 4e78f0b064 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 15:45:23 -04:00
Mark DePristo 8f0badc52b Updating md5s, as the diffobjects walker now emits the summary in reverse order. 2011-07-18 15:44:21 -04:00
Mark DePristo 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. 2011-07-18 15:43:52 -04:00
Mark DePristo 782a05e9b5 Support for sorting the diff output in reverse order. 2011-07-18 15:43:01 -04:00
Mark DePristo 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. 2011-07-18 15:40:15 -04:00
Matt Hanna 15b44ac2c3 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 14:56:41 -04:00
Matt Hanna 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.
 2011-07-18 14:56:00 -04:00
Kiran V Garimella 9eb83bed64 Percentages should be represented as percentages and not, you know, something else. 2011-07-18 14:40:38 -04:00
Matt Hanna adce37774a Add functionality for tsv output. 2011-07-18 14:12:01 -04:00
Eric Banks 6d5e87da10 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 13:59:10 -04:00
Eric Banks 83ba2c066a Making it deterministic 2011-07-18 13:59:02 -04:00
Eric Banks 92fa410450 Check that it's a valid bam file before parsing or bad things can happen 2011-07-18 13:43:34 -04:00
Eric Banks 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). 2011-07-18 13:42:45 -04:00