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6467 Commits (bf6388fa8cdfb59126e4fbf76a642d3cd7d3d870)

Author SHA1 Message Date
Kiran V Garimella bf6388fa8c Print haplotype start locus 2011-07-21 11:06:45 -04:00
Kiran V Garimella 45e536dca8 Reenable haplotype printing 2011-07-21 10:40:40 -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 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