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hammerlab
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guacamole
Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Apache License 2.0
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Revert somatic standard tests to use table properties
#567
arahuja
closed
8 years ago
2
Move to Spark 2.0
#566
arahuja
opened
8 years ago
2
correct tumorl to tumor
#565
arahuja
closed
8 years ago
2
travis scoverage attempt
#564
ryan-williams
closed
8 years ago
10
upgrade to magic-rdds 1.0.0
#563
ryan-williams
closed
8 years ago
0
fix broken docstring
#562
ryan-williams
closed
8 years ago
0
truncate progress-printing of LociPartitioning
#561
ryan-williams
closed
8 years ago
0
Send relevant reference sequences to executors in more fine-grained ways than via a Broadcast
#560
ryan-williams
opened
8 years ago
0
add scripts for printing JAR paths, classpath
#559
ryan-williams
closed
8 years ago
0
restore removed docstrings
#558
ryan-williams
closed
8 years ago
0
scala.version.prefix nits
#557
ryan-williams
closed
8 years ago
1
take sample-id awareness out of read-partitioning code
#556
ryan-williams
closed
8 years ago
1
split more things out of TestUtil
#555
ryan-williams
closed
8 years ago
2
filters cleanup
#554
ryan-williams
closed
8 years ago
1
Allow receiving inputs from config files
#553
ryan-williams
opened
8 years ago
0
rm redundant/obsolete licensing info
#552
ryan-williams
closed
8 years ago
3
Remove `progress` helper, use Spark/log4j
#551
ryan-williams
opened
8 years ago
0
clarify "quiet" param governing partitioning debug info
#550
ryan-williams
closed
8 years ago
1
add load/save capability to PartitionedRegions
#549
ryan-williams
closed
8 years ago
1
Test running on Baylor "case 2" dataset
#548
ryan-williams
opened
8 years ago
2
Include spark application id in VCF metadata in joint caller
#547
timodonnell
closed
8 years ago
2
optionally error/warn on repeat contigs in coverage-depth computation
#546
ryan-williams
closed
8 years ago
1
cache coverages
#545
ryan-williams
closed
8 years ago
2
minor thing: consider changing `--quiet` to indicate performance implications
#544
timodonnell
closed
8 years ago
0
move makeRead from TestUtil to ReadsUtil
#543
ryan-williams
closed
8 years ago
4
mv `jointcaller` pkg to top-level
#542
ryan-williams
closed
8 years ago
1
space out lots of joint caller code blocks
#541
ryan-williams
closed
8 years ago
3
reuse bestAllele in SJC test
#540
ryan-williams
closed
8 years ago
1
Parends nits
#539
ryan-williams
closed
8 years ago
6
drop some unnecessary syntax
#538
ryan-williams
closed
8 years ago
1
fold LikelihoodUtil into LikelihoodSuite
#537
ryan-williams
closed
8 years ago
1
rename SJC test
#536
ryan-williams
closed
8 years ago
1
use per-sample alias in PFMU test
#535
ryan-williams
closed
8 years ago
2
Import some PFMU/WFMU methods directly in tests
#534
ryan-williams
closed
8 years ago
1
makePileup / PileupUtil helper
#533
ryan-williams
closed
8 years ago
3
rm unused LociParser.result() overload
#532
ryan-williams
closed
8 years ago
1
add sort-order comment
#531
ryan-williams
closed
8 years ago
1
rename regions var
#530
ryan-williams
closed
8 years ago
1
name null-ish method params
#529
ryan-williams
closed
8 years ago
1
Comment nits
#528
ryan-williams
closed
8 years ago
1
factor out SJC callPileups
#527
ryan-williams
closed
8 years ago
1
move some var declarations closer to their usages
#526
ryan-williams
closed
8 years ago
1
standardize contigName, contigSequence var names
#525
ryan-williams
closed
8 years ago
1
optimize some Imports
#524
ryan-williams
closed
8 years ago
1
expand some blocks over more lines for legibility
#523
ryan-williams
closed
8 years ago
4
comment typo fixes
#522
ryan-williams
closed
8 years ago
1
rm Pileup.head accessor
#521
ryan-williams
closed
8 years ago
1
PartitionedRegions improvements
#520
ryan-williams
closed
8 years ago
2
rm redundant commons-io dep
#519
ryan-williams
closed
8 years ago
0
fix PileupFlatMapUtils filename typo
#518
ryan-williams
closed
8 years ago
2
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