5e288136e0
Added unit tests for the SnpEff codec, and made minor adjustments to the codec itself.
2011-08-08 16:51:43 -04:00
dd974040af
When finding the highest-impact effect at a locus, all effects that are not within a
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non-coding gene are now considered higher impact than all effects that are within a
non-coding gene.
2011-08-08 13:29:54 -04:00
c1061e994c
Initial support for adding genomic annotations through VariantAnnotator using
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the output from the SnpEff tool, which replaces the old Genomic Annotator.
2011-08-08 13:29:53 -04:00
99e3a72343
Merged bug fix from Stable into Unstable
2011-08-08 12:36:17 -04:00
8072bd9831
Updating resource bundle generation qscript for changeover to git
2011-08-08 12:35:39 -04:00
0db79207e8
Refactored dependancy from CommandLineGATK from javadocs
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This allows us to run the GATK again in environments without Javadoc loading by default in the classpath
2011-08-08 12:27:13 -04:00
0db46d0648
Merged bug fix from Stable into Unstable
2011-08-08 10:50:09 -04:00
2fd101135c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-08 10:49:43 -04:00
4d6cb33612
removing temporary bam index
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The clean bai file was left behind after the data processing pipeline was done
2011-08-08 10:49:28 -04:00
88061ed5fa
rmdir the empty tmp dir if possible
2011-08-08 09:18:20 -04:00
6693407bd8
Merged bug fix from Stable into Unstable
2011-08-07 17:39:03 -04:00
738e94efcb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-07 17:36:45 -04:00
b3e57c329a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-07 15:18:15 -04:00
5f8bc3aa8a
Documenting classes, and name cleanup
2011-08-07 15:17:50 -04:00
1c63d43176
Help now points to GATKDocs instead of spitting out full, garbled description
2011-08-07 15:02:46 -04:00
3c7a96cf2d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-07 12:12:47 -04:00
be0fc8a1e0
Now creates .gz archive of s3 downloads
2011-08-07 12:11:50 -04:00
f534c2e7bb
Merged bug fix from Stable into Unstable
2011-08-06 10:43:52 -04:00
eaa2f16d83
When a job finishes successfully in the ShellJobRunner, mark it as DONE instead of FAILED.
2011-08-06 10:42:04 -04:00
a8eb8c27f0
a) Minor changes to indel consensus scripts to better reflect good default values, b) Fixed up Mills/Devine codec so it always produces correct ref padded bases, and added option to VariantsToVCF to fix reference base
2011-08-04 15:34:49 -04:00
98a96f07c1
Updated standard deviation parameter in VQSR to our current recommended value
2011-08-04 14:06:26 -04:00
406982284c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-04 12:49:02 -04:00
e48492f3c3
Validate that the reference padding base for indels is correct.
2011-08-04 12:48:56 -04:00
f10588420c
Fixing path to dbSNP file as the other one was replaced
2011-08-04 12:36:24 -04:00
21dc9a5543
Adding mills/devine indel dataset to the resource bundle
2011-08-04 12:31:28 -04:00
0739b7f75b
Merged bug fix from Stable into Unstable
2011-08-04 11:07:25 -04:00
aff681e407
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-04 11:05:25 -04:00
fa97bd8ac1
Merged bug fix from Stable into Unstable
2011-08-04 09:52:10 -04:00
23ec5b94cf
fixed a missing check for null
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There was a missed check for the case when you don't provide an indels vcf for the cleaner.
2011-08-04 09:50:02 -04:00
a831af1166
Another misprint when removing the references to -D
2011-08-03 21:29:21 -04:00
8981367307
Updating memory usage for picard programs
2011-08-03 15:48:28 -04:00
f62f47d476
Not sure why this didn't fail before, but bringing VE up to date with previous changes
2011-08-03 14:27:07 -04:00
3de10b1ef8
Fixing misprint from Ryan's commit
2011-08-03 12:37:50 -04:00
db2e0aaa1a
Darn, forgot to update unit tests.
2011-08-03 12:31:08 -04:00
020b2408a8
Adding integration test for left alignment of indels
2011-08-03 12:19:44 -04:00
f6648e0144
Don't left-align complex indels because it's too complicated.
2011-08-03 12:03:50 -04:00
5dc324ff35
Dealing with merge confict
2011-08-03 11:03:47 -04:00
7c89fe01b3
Instead of having the padded reference base be some hackish attribute it is now an actual variable in the Variant Context class. More importantly, we now always require that it be present when padding is necessary - and validate as such upon construction of the VC. This cleans up the interface significantly because we no longer require that a reference base be passed in when writing a VC/VCF record.
2011-08-03 11:00:36 -04:00
3e043a633c
Merged bug fix from Stable into Unstable
2011-08-03 02:23:16 -04:00
a587f38808
Fixed example unified genotyper pipeline to wrap filter expressions with quotes and use rod binding name "variant" instead of "vcf".
2011-08-03 02:21:01 -04:00
5dcac7b064
GATKReport v0.2:
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- Floating point column widths are measured correctly
- Using fixed width columns instead of white space separated which allows spaces embedded in cell values
- Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width
- Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly
Replaced GATKReportTableParser with existing functionality in GATKReport
2011-08-03 00:24:47 -04:00
d3437e62da
Added a simple utility method Utils.optimumHashSize() to calculate the optimum
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initial size for a Java hash table (HashMap, HashSet, etc.) given an expected
maximum number of elements. The optimum size is the smallest size that's
guaranteed not to result in any rehash / table-resize operations.
Example Usage:
Map<String, Object> hash = new HashMap<String, Object>(Utils.optimumHashSize(expectedMaxElements));
I think we're paying way too heavy a price in unnecessary rehash operations across
the GATK. If you don't specify an initial size, you get a table of size 16 that gets
completely rehashed and doubles in size every time it becomes 75% full. This means you
do at least twice as much work as you need to in order to populate your table:
(n + n/2 + n/4 + ... 16 ~= (1 + 1/2 + 1/4...) * n ~= 2 * n
2011-08-02 21:59:06 -04:00
df37716857
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-02 18:27:13 -04:00
daeabe6a2f
Updated HybridSelectionPipelineTest's variant count and titv to match expectations based on ebanks removing strand bias.
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TODO: update filtering/recalibrations in HSP.
2011-08-02 17:09:16 -04:00
20afe2a437
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-02 15:34:52 -04:00
b2cde87378
Removing --DBSNP syntax from BQSR integration tests
2011-08-02 15:34:38 -04:00
c2dc7c9c99
Updated flanks eval the same way the targets eval was updated by ebanks.
2011-08-02 15:30:04 -04:00
c0653514b3
minor update to comment in UG
2011-08-02 13:34:48 -04:00
2ba57bb502
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-02 13:30:46 -04:00
38e4ae4176
minor update to comment in UG
2011-08-02 13:30:38 -04:00
David Roazen
Ryan Poplin
Mark DePristo
Mauricio Carneiro
Khalid Shakir
Guillermo del Angel
Eric Banks