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Author SHA1 Message Date
Ron Levine aace73e884 Enable control of reporting periodicity 2016-07-13 07:24:03 -04:00
Ron Levine 3c5eac8c17 Move htsjdk and picard to version 2.5.0 2016-06-28 09:42:32 -04:00
sooheelee 6fe80d53d0 Improve documentation 
Clarified that this also filters supplementary alignments.
 2016-06-23 16:20:00 -04:00
Samuel Lee 76bb8fd9e5 Allows GatherBqsrReports to accept a .list file as input. 2016-06-22 12:39:18 -04:00
Geraldine Van der Auwera 85dce75f3f Update pom versions to mark the start of GATK 3.7 development 2016-06-01 17:21:48 -04:00
Geraldine Van der Auwera f185a75e1c Update pom versions for the 3.6 release 2016-06-01 17:08:17 -04:00
Geraldine Van der Auwera d87345cd1d GATKDocs overhaul 
- Fixed displaying of default values
    - Removed code cruft
    - Reorganized tooldoc categories and improved names
    - Reorganized tools within categories where applicable
    - Touched up various tool docs
    - Switched default gatkdocs output to html
    - Added parameter in agrregator pom to control output type
    - Set gatkdocs publishing script to output php
    - Deprecated GenotypeAndValidate walker
    - Added back PhoneHome arguments with @Deprecated annotations
 2016-05-29 16:35:08 -04:00
Geraldine Van der Auwera 0769c8ae3e Remove Phone Home 2016-05-27 16:16:29 -04:00
Geraldine Van der Auwera 5b80c92cb7 Improved article linking in error messages 2016-05-27 13:49:31 -04:00
Geraldine Van der Auwera 3b7e0c56bf Moved post-IR MQ reverter filter to public 2016-05-27 12:39:58 -04:00
Ron Levine 35a06879f1 Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -04:00
Geraldine Van der Auwera 14fe8b1e0e Moved BQSRGatherer and dependencies to the public module 2016-04-27 07:15:28 -04:00
Ron Levine f337b45724 Move htsjdk and picard to version 2.0.0 
Conflicts:
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
 2016-04-25 14:51:25 -04:00
Yossi Farjoun b471884d97 Added run-time information to log output 
Also updated copyright date
 2016-03-11 16:43:03 -05:00
Geraldine Van der Auwera 9a306ca221 Update licenses 2016-03-05 01:09:43 -08:00
Geraldine Van der Auwera 2b70f14740 Misc documentation improvements 
Added caveat to VariantFiltration documentation
  Fixed PON creation example in M2 doc
  Improved MalformedReadFilter doc
  Updated N CIGAR error message
 2016-03-03 15:48:54 -08:00
Ron Levine ed933013fe Remove variant contig order check 2016-01-16 19:32:28 -05:00
Geraldine Van der Auwera 4767a83d8a Update pom versions to mark the start of GATK 3.6 development 2015-11-25 01:52:51 -05:00
meganshand 2570cab24c Assorted documentation fixes, enhancements and reorganization. 
See issues referenced by the pull request for details.
 2015-11-20 22:44:46 -05:00
Ron Levine 0b3b09e3ff Move htsjdk & picard to version 1.141 2015-11-20 16:26:26 -05:00
Ron Levine ccaddefa19 Validate VCF with sequence dictionary 2015-11-20 09:23:24 -05:00
Mark Fleharty 19af5724c5 Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden 2015-10-27 09:44:26 -04:00
Chris Norman e776502c49 Fix Sample mergeValues failure when merging identical string values (#1156). 2015-10-12 09:56:05 -04:00
Ron Levine 3ecabf7e45 Allow overriding ValidateVariants' hard-coded cutoff for allele length 2015-09-17 10:49:14 -04:00
Khalid Shakir 24e24b9468 Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`. 
Updated other IntelliJ IDEA warnings in GATKBAMIndex.
Updated example .cram files to match versions generated by current GATK/HTSJDK.
Bumped HTSJDK and Picard to 1.139 releases.
Added support for using `-SNAPSHOT` of HTSJDK in the future.
 2015-09-14 12:20:36 -04:00
Mark Fleharty daeb55429e Adding Static Binning to BQSR 2015-08-24 13:36:17 -04:00
Ron Levine beec624a63 Move htsjdk & picard to rev 1.138 2015-08-20 10:42:25 -04:00
Yossi Farjoun 69fd4af15a Merge pull request #1111 from jsilter/overclippedreadfilter_endsoption 
Add additional option to OverclippedReadFilter
 2015-08-12 10:43:52 -04:00
Jacob Silterra 62625b4bc6 Add option to not require soft-clips on both ends 
Previous version of OverclippedReadFilter would only filter a read if both ends of a read had a soft-clipped block.
This adds a boolean option to relax that requirement, and only require 1 soft-clipped block, while also filtering on read length - softclipped length
 2015-08-12 10:38:27 -04:00
Khalid Shakir 9bee183f6c Switched to using CRAM's SamReader.Indexing implementation. 
CRAM now requires .bai index, just like BAM.
Test updates:
- Updated existing MD5s, as TLEN has changed.
- Tests multiple contigs.
- Tests several intervals per contig.
- Tests when `.cram.bai` is missing, even when `.cram.crai` is present.
Updated gatk docs for CRAM support, including:
- Arguments that work for both BAM and CRAM listed as such.
- Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM".
- Instructions on how to recreate a `.cram.bai` using cramtools.
Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.
 2015-08-11 17:52:49 -03:00
Geraldine Van der Auwera 19bbe45cbc Updated licenses for 2015 2015-08-06 15:23:11 -04:00
Geraldine Van der Auwera 719bb15340 Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz 
Indexing parameters not required if output file has the g.vcf.gz exte…
 2015-06-17 14:30:20 -04:00
Ron Levine b35085ca28 Indexing parameters not required if output file has the g.vcf.gz extensionv 2015-06-13 11:46:56 -04:00
Ron Levine dbed660183 Add spannning deletions allele 2015-06-12 16:43:06 -04:00
Eric Banks 8c81e7df95 Added a new filter that can be used to remove reads that are too small and overly clipped. 2015-05-22 14:33:35 -04:00
Geraldine Van der Auwera d1a7edd796 Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
Geraldine Van der Auwera f19618653a Update pom versions for the 3.4 release 2015-05-15 00:40:39 -04:00
David Roazen caafe84e74 Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central 
-We now pull htsjdk and picard from maven central.

-Updated the GATK codebase as necessary to adapt to changes in the Feature
 interface.

-Since VCFHeader now requires that all header lines have unique keys, uniquified
 the keys of GVCFBlock header lines by including the min/max GQ in the key.
 Updated MD5s accordingly.

-Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
 2015-05-14 15:26:23 -04:00
Geraldine Van der Auwera 919c3eaa2e Numerous doc fixes; mostly formatting and clarifications 2015-05-03 00:28:46 +02:00
Ron Levine d5f98e99f0 Bypass reads with a bad CIGAR length 2015-04-21 11:55:56 -04:00
Alex Baumann 024ec69e97 Modify GATK command line header for unique keys 
The GATK command line header keys were being repeated in the VCF and
subsequently lost to a single key value by HTSJDK.  This resolves
the issue by appending the name of the walker after the text
"GATKCommandLine" and a number after that if the same walker was
used more than once in the form: GATKCommandLine.(walker name) for
the first occurrence of the walker, and GATKCommandLine.(walker name).#
where # is the number of the occurrence of the walker (e.g.
GATKCommandLine.SomeWalker.2 for the second occurrence of SomeWalker).
Integration test added to EngineFeaturesIntegrationTest to verify
two runs of same walker follow expected form.

Resolves #909
See also: HTSJDK #43
 2015-04-02 13:56:11 -04:00
Ron Levine aef0a83c52 Automatically choose indexing strategy by file extension 2015-03-27 11:10:35 -04:00
Phillip Dexheimer 3b567d7a98 Fixed logging of 'out' command line parameter in VCF headers 2015-03-18 23:12:13 -04:00
Phillip Dexheimer 6ffa295963 Regression: The new 'includeUnmapped' PartitionBy annotation was incorrectly set for HC 
Fixes #828
 2015-03-13 00:24:57 -04:00
Ron Levine 71d68c3d93 Fix NotPrimaryAlignmentFilter documentation 2015-03-05 20:30:46 -05:00
Geraldine Van der Auwera f3a57a6b07 Merge pull request #811 from broadinstitute/seru71_fix_MateSameStrandFilter 
Corrected logical expression in MateSameStrandFilter
 2015-02-23 17:57:10 -05:00
Ron Levine 2cbaef2fb2 Throw exception for -dcov argument given to ActiveRegionWalkers 2015-02-19 08:24:39 -05:00
seru71 3ee0311fdb corrected logical expression in MateSameStrandFilter 
Signed-off-by: David Roazen <droazen@broadinstitute.org>
 2015-02-12 12:21:44 -05:00
Phillip Dexheimer 3354c07b1c Added optional element "includeUnmapped" to the PartitionBy annotation 
* The value of this element (default true) determines whether Queue will explicitly run this walker over unmapped reads
 * This patch fixes a runtime error when FindCoveredIntervals was used with Queue
 * PT 81777160
 2015-01-31 15:47:57 -05:00
Khalid Shakir 1808c90d2a Added introductory CRAM support. 
Replaced usage of GATKSamRecordFactory with calls to wrapper GATKSAMRecord extending SAMRecord.
Minor other updates for test changes.
Added exampleCRAM.cram generated by GATK, with .bai and .crai indexes generated by CRAMTools.
CRAM-to-CRAM test disabled due to https://github.com/samtools/htsjdk/issues/148
Using exampleBAM.bam input, outputs of GATK's generated CRAM match CRAMTools generated CRAM, but not samtools/PrintReads SAM output, as things like insert sizes are different.
If required for other tools, CRAM indexes must be generated via CRAMTools until we can generate them via CRAMFileWriter.

Generation of exampleCRAM.cram:
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram --bam-style-index

CRAM generation by existing tools:
* samtools view -C -T public/gatk-utils/src/test/resources/exampleFASTA.fasta -o testSamtools.cram public/gatk-utils/src/test/resources/exampleBAM.bam
* java -jar cramtools-2.1.jar cram --ignore-md5-mismatch --capture-all-tags -Q -n -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -O testCRAMTools.cram
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o testGATK.cram

CRAMTools view of the above:
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleCRAM.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testSamtools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testCRAMTools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testGATK.cram | tail -n 1
 2015-01-26 14:47:39 -03:00