3e9ad4bbd0Porting SAM pileup ROD to Tribble as a case study.
hanna
2010-05-13 00:22:59 +0000
6839c194cbalthough holding on to memories can be fun, it's bound to hurt performance.
aaron
2010-05-12 19:26:58 +0000
c81b910f73Commenting out the parallelization test which is failing
ebanks
2010-05-12 18:39:53 +0000
cac98ba5efa couple of small documentation fixes
aaron
2010-05-12 17:40:27 +0000
2a803e9044simple tool that takes two dbSNP files and subsets the seconds to only include rsID SNPs present in the first. Used to make b129 against b37 by subsetting b131/b37 vs. b129/b36
depristo
2010-05-12 13:39:09 +0000
d3c33d4b3fmore powerful management routines for my pipeline
depristo
2010-05-12 13:37:39 +0000
3f07611187Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes
depristo
2010-05-12 13:36:31 +0000
2c55ac1374fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.
aaron
2010-05-12 06:13:26 +0000
6868ce988fFix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite loop.
hanna
2010-05-11 17:31:19 +0000
34969f304cAdding dbsnp to all UG performance tests
ebanks
2010-05-11 15:48:05 +0000
140e43b93bChecking in to see whether it fails. If I start getting bombarded with Bamboo error reports, I'm commenting it out...
ebanks
2010-05-11 15:39:42 +0000
572b383fe2Make VA annotate dbsnp again
ebanks
2010-05-11 14:06:53 +0000
b09e7231d1A quick implementation of the experimental covariates for the TGen folks to work with.
rpoplin
2010-05-11 01:08:52 +0000
aec5f7b630Can now threshold results based on minimum base and/or mapping quality.
kiran
2010-05-10 19:58:07 +0000
f120a00433Fixed bug so that the strand, alternate, and reference columns are now moved correctly
weisburd
2010-05-10 17:59:39 +0000
f36726554fAppropriate build statements for 'MarkAllAlignmentsAsPrimary' and 'RepairSeattleBAM' - both one-off tools.
kiran
2010-05-10 15:17:51 +0000
13fd182b7cFor dealing with slightly malformatted BAMs - mark every alignment as primary, or in the case of some BAM files from UWash, supply the sample information for each read group.
kiran
2010-05-10 15:17:05 +0000
4a7902bb8eBases 'A' and 'a' (etc.) no longer considered different.
kiran
2010-05-10 14:53:38 +0000
b223b04331Don't list '.' as an alternate allele, dummy!
kiran
2010-05-10 14:51:18 +0000
98718d0faaComputes the error rate per cycle
kiran
2010-05-10 14:50:22 +0000
7527f950d1Computes the quality score distribution per readgroup (one column per readgroup)
kiran
2010-05-10 14:49:38 +0000
c111c15072Computes the distribution of insert size per library (for now, one output file per library)
kiran
2010-05-10 14:48:35 +0000
a51bd57566First version of the smart batch merging tool.
ebanks
2010-05-10 02:18:48 +0000
33a9549896Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian.
rpoplin
2010-05-09 16:48:07 +0000
76efa757f0Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder which improved startup time 5-10x when dynamically merging many BAMs.
hanna
2010-05-08 14:12:22 +0000
d6b036cdabMinor improvements to simple python code
depristo
2010-05-07 21:34:46 +0000
504103bd15Misc. additions to correct utilities
depristo
2010-05-07 21:34:18 +0000
64ccaa4c6aWalkers and integration tests that calculate and compare callable bases
depristo
2010-05-07 21:33:47 +0000
d070554329A walker that calculates read lengths, number and size of clipping events
depristo
2010-05-07 21:32:51 +0000
1749a49042Mapping and base quality thresholds for DoC default to none
chartl
2010-05-07 18:08:13 +0000
7d2df3f511example windowed ROD walker for Kristian, and updates to Tribble
aaron
2010-05-07 17:12:50 +0000
57f254b13aVE integration test
rpoplin
2010-05-07 13:58:25 +0000
7cab994d88Add argument to sortByRef for specifying the tmp directory for sorting. Update the liftover script to reflect this addition.
ebanks
2010-05-07 13:53:26 +0000
44de92e09dChecking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark.
ebanks
2010-05-07 12:31:56 +0000
18f1d31a22Moving to and organizing in core.
ebanks
2010-05-07 04:05:36 +0000
06ea65e60bagain for JIRA GSA-320
aaron
2010-05-07 03:47:58 +0000
ac9b32db88a bug fix for Kiran; putting JIRA in for better type determination system for the new Tribble tracks so this doesn't happen again.
aaron
2010-05-07 03:31:43 +0000
4e0019b04fRepair code that sorts and merges intervals.
hanna
2010-05-06 22:37:25 +0000
72e030a670require that snps be biallelic before we pass them to the TiTv calculation.
aaron
2010-05-06 22:33:00 +0000
3b52ac67e0adding the Tribble codecs to the package.
aaron
2010-05-06 21:06:15 +0000
7cecec7d00Removing zero no-calls restriction in AC stats
rpoplin
2010-05-06 18:55:07 +0000
0e58fb7cc0Moved over to be a walker inside the GATK
ebanks
2010-05-06 18:28:03 +0000
78409dca0dturned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.
aaron
2010-05-06 16:36:58 +0000
bacc507a48Don't worry about sorting anymore in the liftover tool. That will come later.
ebanks
2010-05-06 15:00:30 +0000
d91b27aca1updating Tribble with VCF changes from Eric
aaron
2010-05-06 04:03:21 +0000
5df0361bd2trivial removal of unnecessary comments
ebanks
2010-05-06 03:51:14 +0000
2975e3a4e8picard Intervals don't sort right - switching to GenomeLocs
ebanks
2010-05-06 03:50:28 +0000
7467ec2fd6updating the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to the reflections library people.
aaron
2010-05-06 02:08:41 +0000
1a99fb9318First pass at liftover tool. Passing buck over to Aaron...
ebanks
2010-05-05 20:38:19 +0000
a0d71540dfspeed-up for VCF, adding code to the VCF reader to automagically make an index if one doesn't already exist, and a change to the VCF writer unit test
aaron
2010-05-05 20:19:42 +0000
6bbcc47b5dremoving some out-of-date RODs and some unused genotype writer formats
aaron
2010-05-05 19:07:13 +0000
c998c48a23adding code to detect out-of-date index files, which we now remove and regenerate if the target file is newer than the index file.
aaron
2010-05-05 17:55:36 +0000
a68f3b2e9cVCF moved over to tribble.
aaron
2010-05-05 17:28:48 +0000
ad11201235adding more ROD pile-up tests
aaron
2010-05-05 16:01:11 +0000
0338345beeFixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.
asivache
2010-05-05 15:42:27 +0000
64640d6b17Complete the switch statement to deal with all possible cigar operators for Kris.
ebanks
2010-05-05 13:41:05 +0000
f75e54e3f7fixes for new package names in tribble 74
aaron
2010-05-05 05:47:04 +0000
97dd04cbf0updating Tribble ahead of the big VCF commit
aaron
2010-05-05 05:17:54 +0000
617542853fWalker that can be used with refGene and a TCGA bed file to annotate intervals in an interval list with the genes and exons they overlap.
chartl
2010-05-05 02:55:01 +0000
354262eabeNew convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit.
chartl
2010-05-05 02:54:18 +0000
d5b675b3e6Added - Q&D script to gather verbose bed files to a VCF.
chartl
2010-05-05 02:49:16 +0000
03bea70f3aFixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read.
ebanks
2010-05-04 16:49:21 +0000
510b3efcc2Fixed an issue where asking for the alternate alleles at hom-ref sites would result in an array out-of-bounds exception.
kiran
2010-05-03 18:46:33 +0000
a462b5e1e7Changed a default path
weisburd
2010-05-03 17:07:21 +0000
94b51de401HLA caller updated to examine class II loci, updated pointers to dictionary, allele frequencies.
sjia
2010-05-03 14:54:52 +0000
97fdd92e7bClean up the code to have a unified approach to calculating p(true) for both with and without ti/tv models
rpoplin
2010-05-03 13:30:20 +0000
f497213933DbSNP moved over to tribble
aaron
2010-05-03 06:02:35 +0000
447081583arev tribble with updated version
aaron
2010-05-03 04:07:28 +0000
9d01670f62Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations.
rpoplin
2010-05-02 19:21:23 +0000
9dff578706Added PG tag to bam header to let people know it's been cleaned.
ebanks
2010-04-30 17:30:30 +0000
28f746b76aAdded option to generate UCSC or NCBI sequence
weisburd
2010-04-30 17:26:00 +0000
0e10359a5eOkay, finished up the ability to cap a base's qual by its read's mapping quality. This is experimental - I have not tested its performance on SNP calling, or even played around with it. If you want to test it out, go nuts. But don't come running to me if your results are not good.
ebanks
2010-04-30 16:58:30 +0000
850f36aa61Changes to the Unified Genotyper's arguments:
ebanks
2010-04-30 16:44:24 +0000
8b2ce128b5Optimized the join(..) method.
weisburd
2010-04-30 15:55:07 +0000
c214056d88Script for concatenating results of GenerateTranscriptToInfo.py into one big file
weisburd
2010-04-30 15:47:08 +0000
8bb15ef812Checking in the reference implementation of the downsampler for back comparison.
hanna
2010-04-30 15:41:13 +0000
0069cb426dScript for spawning LSF jobs that run the TranscriptToInfo.java walker on each of the 50 contigs.
weisburd
2010-04-30 15:27:52 +0000
5d5c7f9d34Changed short code of stop codon to 'stop'
weisburd
2010-04-30 13:55:52 +0000
cbed0b1adeAdding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.
aaron
2010-04-29 22:50:17 +0000
7fbfd34315adding the GELI ROD validation
aaron
2010-04-29 21:43:00 +0000
82818a417bAllow header fields to come in any order...
chartl
2010-04-29 18:33:10 +0000
4617abf1ffFix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file.
hanna
2010-04-28 20:42:04 +0000
b648e89096updating Tribble with a bunch of bug and performance fixes found while performance testing GeliText in the GATK
aaron
2010-04-28 18:45:10 +0000
e2ff4167afAdded "#Family ID" as a possible header value for PlinkRod ... since that's in the new sequenom headers for pilot 3 validation
chartl
2010-04-28 18:38:33 +0000
5dce16a8f1Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row.
depristo
2010-04-28 13:10:11 +0000
64c5f287c5fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections
aaron
2010-04-27 17:46:46 +0000
ca649d13aaAdding the post-processing indel filter to GATK
ebanks
2010-04-27 14:43:39 +0000
c647153b10Adding Jama for Ryan.
aaron
2010-04-27 14:30:36 +0000
f6468f9143a fix for a bug we've worked around in the reflections package: previously it didn't find classes that weren't in the main jar. Fixed in this version.
aaron
2010-04-27 04:49:49 +0000
bf3dbd8401some useful routines for working with project processing. madPipeline contains a bunch of useful routines for building pipelines that I finally put into one file. Let's just say that I'm really looking forward to the new pipeline system...
depristo
2010-04-26 12:34:04 +0000
hanna
aaron
ebanks
depristo
rpoplin
kiran
weisburd
chartl
asivache
sjia