18728ec5bdUpdates to the bundle script: 1. Add the symbolic 'current' link for the new bundle dir 2. Don't gzip and copy .out files 3. Don't call chr20 SNPs on the example BAM because it's now just a few reads on chr1
Eric Banks
2012-12-18 11:16:42 -0500
16eb1c5436Optimization to TraverseReadsNano
Mark DePristo
2012-12-17 16:40:04 -0500
b33f804cdcInline increment function in RecalDatum to avoid minor duplication of work and multiple synchronized method calls
Mark DePristo
2012-12-17 16:38:10 -0500
66d32f646bMinor cleanup of BAQ calculation (final variables, etc)
Mark DePristo
2012-12-17 16:37:20 -0500
67fe81391cProgressMeter optimization: don't do genome loc formatting, but instead create an object that only formats when printing is actually needed
Mark DePristo
2012-12-17 15:55:21 -0500
1de2f527b9Optimization of recalibrateRead
Mark DePristo
2012-12-13 17:21:36 -0500
bd6cda7542Trivial optimization of TraverseReadsNano -- don't format the shard toString if logger isn't debug enabled
Mark DePristo
2012-12-12 16:21:43 -0500
a481d006f0Optimizations for applying BQSR table with PrintReads
Mark DePristo
2012-12-12 16:14:09 -0500
5ec25797b3Optimizations for BaseRecalibrator
Mark DePristo
2012-12-12 13:54:14 -0500
6cb1a0a698Avoid db naming collisions when running multiple instances of na12878kb tests concurrently
David Roazen
2012-12-17 16:13:03 -0500
e6f468b647Refactored the quasi-useful IndelType annotation into the more useful VariantType. The indels are still annotated as before, but now all other variant types are annotated too. I'm doing this because of requests on the forum but am not making it standard. If we find it to be useful we can turn it on by default later.
Eric Banks
2012-12-17 11:54:47 -0500
6171419e6cMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2012-12-17 11:27:52 -0500
98f18b5f9eChanging the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.
Ryan Poplin
2012-12-17 11:27:44 -0500
40b3941678Merge pull request #7 from jsilter/master
depristo
2012-12-17 08:05:55 -0800
762f184262Bug fix for strict validation: rsID checking wasn't working if there were multiple IDs
Eric Banks
2012-12-17 10:32:41 -0500
1d18ee26ccMerge remote-tracking branch 'unstable/master'
Eric Banks
2012-12-17 09:03:03 -0500
ea704d688fchose smaller buffer size for the bufferedStream
Yossi Farjoun
2012-12-15 13:01:38 -0500
6da2338ea7removed comments and uneeded imports
Yossi Farjoun
2012-12-15 12:31:37 -0500
8198414352Add removeCall, which removes all calls matching the provided MongoVariantContext. _id and Date fields are excluded. Generally intended te remove only a single call
Jacob Silterra
2012-12-14 13:07:44 -0500
5f1afb4136Fixing an off-by-one clipping error in ReduceReads for reads off the contig
Mauricio Carneiro
2012-12-13 21:56:44 -0500
74344a3871Bringing in the changes from the CMI repo
Mauricio Carneiro
2012-12-13 21:59:37 -0500
696bf95fbaFix for PBT bug reported on the forum: the AD is actually output correctly now (rather than with 'null' or some gibberish memory pointer).
Eric Banks
2012-12-13 23:28:30 +0000
aeab932c63Actual working version of unflushing VCFWriter
Mark DePristo
2012-12-13 12:24:08 -0500
97e880654bBug fix in setting output file names
Guillermo del Angel
2012-12-13 15:08:22 -0500
021929788cDon't compress intermediate BAMs, will save time
Guillermo del Angel
2012-12-12 17:40:25 -0500
5e66109268Replaced a useless getInt with a skipInt to remove 1/4 of the initial seek time in the BAM Index.
Yossi Farjoun
2012-12-12 15:26:38 -0500
5780926254Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2012-12-12 15:42:40 -0500
62eaffdf0aFix docs for ReadBackedPhasing
Eric Banks
2012-12-12 20:28:04 +0000
bba63a3b0eFix for GSA-615: UnifiedGenotyperEngine.getGLModelsToUse takes 5% of the runtime of UG, should be optimized away.
Eric Banks
2012-12-12 20:25:45 +0000
211a6e78eaFurther related bug fixes to GGA mode in the HC: some variants (especially MNPs) were causing problems because they don't have to start at the current location to match the allele being genotyped. Fixed.
Ryan Poplin
2012-12-12 14:53:02 -0500
33290bfe0cAdded integration test to catch the read off contig in ReduceReads.
Mauricio Carneiro
2012-12-12 13:41:01 -0500
a52e3c7e15Revert "Bug fix for RR: don't let the softclip start position be less than 1" this introduced a bug in reduce reads by de-activating it's hard clipping of the out of bounds soft-clips (specially in the MT). DEV-322 #resolve #time 4m
Mauricio Carneiro
2012-12-12 13:09:39 -0500
5632c13bf2Resolves GSA-681 / Compressed VCF.gz output is too big because of unnecessary call to flush().
Mark DePristo
2012-12-12 10:27:07 -0500
216f92276cDisable scatter-gather with PrintReads since we're already setting high nct so it's unnecessary
Guillermo del Angel
2012-12-12 09:06:37 -0500
0e5b1093fbinitial implementation of contamination estimation, tested on single gene (which doesn't have enough data) waiting to test on exome/chr20
Kristian Cibulskis
2012-12-11 15:59:59 -0500
dd52a70d45Fix AFCalcResult unit test
Mark DePristo
2012-12-11 10:39:58 -0500
6bf31065e3Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2012-12-11 10:34:50 -0500
2f99569ddachange the md5 in one of the CV intergration tests, since it wasn't use the priority list when printing the origin of the annotation (the setValue field)
Ami Levy-Moonshine
2012-12-10 22:48:15 -0500
2e3284f306Continue to fix the case where PRIORITIZE is used but no priority list is given. While fixing that case I also removed unnecessary sorting, when the prioeity list is not provied. When the priority list is not provided, it will continue to be null. Thus, the number of original Variant Contexts should be given as a new parameter to simpleMerge (since priority might be null). This new parameter is used for checking if there are filtered VC, when annotationOrigin is true.
Ami Levy-Moonshine
2012-12-10 22:23:58 -0500
8a115edbafReduceReads is now scattered by contig
Mauricio Carneiro
2012-12-06 17:06:32 -0500
bdda63d973Related bug fixes to GGA mode in the HC: some variants (especially MNPs) were causing problems because they don't have to start at the current location to match the allele being genotyped. Fixed.
Eric Banks
2012-12-10 14:47:04 -0500
ceb5431dcbMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2012-12-10 12:24:47 -0500
c84ff9d75eAdding explicit true negative assessment category to the AssessNA12878 walker.
Ryan Poplin
2012-12-10 12:24:43 -0500
573ace4403restore the right version of VariantContextUtils.java in my unstable dir
Ami Levy-Moonshine
2012-12-10 10:28:56 -0500
46edab6d6aUse the new downsampling implementation by default
David Roazen
2012-11-26 12:44:48 -0500
5460c96137Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2012-12-09 23:43:57 -0500
3a420d163e(1) changes in catVariants (work still under development) (2) changes to CV to throw an error when GenotypeMergeType is PRIORITIZE but no priority (rod_priority_list) is not given. Reported by TechnicalVault on the forum on Nov 14 2012
Ami Levy-Moonshine
2012-12-09 23:40:03 -0500
2637f512f8Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2012-12-09 02:09:40 -0500
574d5b467fBug fix for indel HMM: protect against situation where long reads (e.g. Sanger) in a pileup can lead to a read starting after the haplotype end for a given haplotype.
Eric Banks
2012-12-09 02:09:34 -0500
9b6ee0576fFix bugs in the consensus genotype creation algorithm for the NA12878 KB
Mark DePristo
2012-12-08 13:18:07 -0500
bf8421eeb7Fixes GSA-671 / AFCalcResult.log10pNonRefByAllele should really be log10pRefByAllele
Mark DePristo
2012-12-07 16:02:58 -0500
3355216366Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2012-12-07 15:35:17 -0500
9573648f85Changes to count the sites which might be present in some of the input rods but not present at all in other rods. Now loop over the input rod names instead of looping over the tracker results.
Ryan Poplin
2012-12-07 15:35:08 -0500
3b0e3767bfAdd a test for a read that extends off the end of chr1
Joel Thibault
2012-12-07 13:46:41 -0500
58e39a8468Enabling 4-way parallel by default in FastQ2BAM DEV-317
Mauricio Carneiro
2012-12-06 17:24:09 -0500
cc4e3ec589Update TODO list
Joel Thibault
2012-12-05 12:45:02 -0500
abd94b2976Bugfix for handling invalid records in NA12878 KB
Mark DePristo
2012-12-06 10:24:24 -0500
406adb8d44The allele biased downsampling should not abort if there's a reduced read. Rather it should always keep the RR and downsample only original reads in the pileup.
Eric Banks
2012-12-05 23:15:36 -0500
6d22f4f737Bringing latest performance updates from the GATK to CMI
Mauricio Carneiro
2012-12-05 21:40:03 -0500
dbf721968dPrintReads large-scale test to protect against another major low-level performance issue
Mark DePristo
2012-12-05 21:35:27 -0500
00c23bf704Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2012-12-05 15:53:05 -0500
234ff64556Changes to AssessNA12878 to allow for 100s of input callsets to assess against the database.
Ryan Poplin
2012-12-05 15:52:57 -0500
5d78a61f7aMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2012-12-05 15:07:12 -0500
d0cab795b7Got caught in the middle of a bad integration test, that was fixed in independent push. Moved test bam into testdata.
Mark DePristo
2012-12-05 14:49:01 -0500
465694078eMajor performance improvement to the GATK engine
Mark DePristo
2012-12-04 22:08:01 -0500
2b601571e7Better error handling in NanoScheduler
Mark DePristo
2012-12-04 20:59:07 -0500
51dbb562c9Reduce amount of debugging information from NA12878KnowledgeBaseServer
Mark DePristo
2012-12-02 16:46:07 -0500
efe256ec09binary search implementation to find the minimum coverage
Mauricio Carneiro
2012-12-05 12:19:07 -0500
430d6a07f2Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2012-12-05 11:20:28 -0500
0c925856cbMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2012-12-05 02:00:39 -0500
ef87b18e09In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then).
Eric Banks
2012-12-05 02:00:35 -0500
13896356adAdded bootstrapping and fixed the GLM model of the FMCC
Mauricio Carneiro
2012-12-05 01:06:19 -0500
30f013aeb0Added a copy() method for ReadBackedPileups
Mauricio Carneiro
2012-12-04 23:56:30 -0500
6feda540a4Better error message for SimpleGATKReports
Mauricio Carneiro
2012-12-04 23:55:35 -0500
726332db79Disabling the testNoCmdLineHeaderStdout test in UG because it keeps crashing when I run it locally
Eric Banks
2012-12-05 00:54:00 -0500
61bde6210bRestored RemoteFile push and pull in base QScript.
kshakir
2012-12-04 12:32:00 -0500
8d2d0253a2introduce a level of indirection for the forum URLs - this new function will allow me a place to morph the URL into something that is supported by Confluence
Randal Moore
2012-12-03 12:54:48 -0600
1af41754e3Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2012-12-03 22:01:11 -0500
bca860723aUpdating tests to handle bad validation data files (that used the wrong qual score encoding); overrides push from stable.
Eric Banks
2012-12-03 22:01:07 -0500
387c0defeddon't change md5 here because I am handling it separately from unstable with a better command-line in the test
Eric Banks
2012-12-03 21:49:45 -0500
ef95757311Fix MD5 because of a need to fix a busted bam file in our validation directory (it used the wrong quality score encoding...)
Eric Banks
2012-12-03 21:46:46 -0500
4ced2e4ffcMerge branch 'develop' of github.com:broadinstitute/cmi-gatk into develop
Guillermo del Angel
2012-12-03 20:14:43 -0500
c2c6b858e3Better checks/more flexibility in fastq2bam parsing. Immediate benefit: we can now process normal-only samples, and metadata should be able to specify tumor/normal pairs in any order. Hard-coded hacks removed. DEV-134 #resolve #time 3m
Guillermo del Angel
2012-12-03 20:14:37 -0500
472381245aAllow for more refined control of memory and queues to run with
Menachem Fromer
2012-12-03 17:07:03 -0500
67932b357dBug fix for RR: don't let the softclip start position be less than 1
Eric Banks
2012-12-03 15:59:14 -0500
d5ed184691Updating the HC integration test md5s. According to the NA12878 knowledge base this commit cuts down the FP rate by more than 50 percent with no loss in sensitivity.
Ryan Poplin
2012-12-03 15:38:59 -0500
a47da9bb2fMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2012-12-03 14:30:14 -0500
156d6a5e0bmisc minor bug fixes to GenotypingEngine.
Ryan Poplin
2012-12-03 12:47:35 -0500
5fed9df295Quick fix: base qual array in the GATKSAMRecord stores the actual phred values (-33) and not the original bytes (duh).
Eric Banks
2012-12-03 12:18:20 -0500
b6839b3049Added checking in the GATK for mis-encoded quality scores.
Eric Banks
2012-12-03 11:18:41 -0500
18b002c99cMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2012-12-03 10:08:56 -0500
6f523a1ea0Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2012-12-03 08:41:21 -0500
59fc7456cfUpdated expectations for novel TiTv in HSP after Mark's fixes to the exact model
Eric Banks
2012-12-03 08:41:13 -0500
f0a4710247Callset summary now includes a table for the consensus itself
Mark DePristo
2012-12-02 16:40:12 -0500
ce9a323c04NA12878 knowledge base automatically filters duplicate records out in the SiteIterator
Mark DePristo
2012-12-02 14:21:29 -0500
1bdf17ef53Reworking of how the likelihood calculation is organized in the HaplotypeCaller to facilitate the inclusion of per allele downsampling. We now use the downsampling for both the GL calculations and the annotation calculations.
Ryan Poplin
2012-12-02 11:58:32 -0500
1828d33a5aBugfix to AssessNA12878
Mark DePristo
2012-12-02 11:09:15 -0500
Eric Banks
Mark DePristo
David Roazen
Ryan Poplin
Yossi Farjoun
Jacob Silterra
Mauricio Carneiro
Guillermo del Angel
Chris Hartl
Kristian Cibulskis
Ami Levy-Moonshine
Joel Thibault
kshakir
Randal Moore
Menachem Fromer