hammerlab guacamole issues

hammerlab / 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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issues

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upgrade hammerlab/spark-genomics deps

#617 ryan-williams opened 7 years ago
2
Get guacamole and friends building on newest batch of shared libraries

#616 hammer opened 7 years ago
1
Make indel realignment splice aware

#615 hammer opened 7 years ago
1
port to SBT, factor out more components, upgrade some deps

#614 ryan-williams closed 7 years ago
3
Factor out some reusable components to other repos

#613 ryan-williams closed 7 years ago
1
Upgrades and default settings to SomaticStandard

#612 arahuja closed 7 years ago
5
--loci argument conflicts with TakeLociIterator

#611 arahuja opened 8 years ago
2
add --split-size arg

#610 ryan-williams closed 8 years ago
6
rm some test boilerplate

#609 ryan-williams closed 8 years ago
1
Add loci set intersection and difference methods

#608 arahuja closed 8 years ago
5
clean up test-kryo-registrations

#607 ryan-williams closed 8 years ago
2
loci-parsing refactor

#606 ryan-williams closed 8 years ago
2
Remove PileupFilter and revamp InputFilters

#605 arahuja closed 8 years ago
3
add PartitionReads cmd

#604 ryan-williams closed 8 years ago
2
add `partition-loci` cmd

#603 ryan-williams closed 8 years ago
2
ReferenceBroadcast improvements

#602 ryan-williams closed 8 years ago
1
fix DeBruijnGraph filename typo

#601 ryan-williams closed 8 years ago
1
fold AffineGapPenaltyAlignment into ReadAlignment

#600 ryan-williams closed 8 years ago
3
remove method-access boilerplate

#599 ryan-williams closed 8 years ago
3
allow spark confs as cmdline flags

#598 ryan-williams closed 8 years ago
1
fold halfWindowSize into args plumbing

#597 ryan-williams closed 8 years ago
3
rm ParRegArgs from ReadSets args

#596 ryan-williams closed 8 years ago
1
LociPartitioning cleanups

#595 ryan-williams closed 8 years ago
3
scala 2.11 forward-compat fixes and misc build tweaks

#594 ryan-williams closed 8 years ago
1
use coarser loci-ranges in TakeLociIterator

#593 ryan-williams closed 8 years ago
6
rm unused DebugLogArgs

#592 ryan-williams closed 8 years ago
1
test-script refactor

#591 ryan-williams closed 8 years ago
2
rm broken .array call

#590 ryan-williams closed 8 years ago
4
lots of pom, shading, scripts improvements

#589 ryan-williams closed 8 years ago
3
Can't use guacamole in spark-shell due to guava-shading nuances

#588 ryan-williams closed 8 years ago
0
improvements / bugfix in capped-regions partitioner

#587 ryan-williams closed 8 years ago
2
shade breeze

#586 ryan-williams closed 8 years ago
3
Breeze NoSuchMethodError

#585 ryan-williams closed 8 years ago
9
bump shade plugin version, fix assembly build

#584 ryan-williams closed 8 years ago
2
Error when packaging uber jar

#583 e5c closed 8 years ago
0
port POM to org.hammerlab:scala-parent-pom

#582 ryan-williams closed 8 years ago
2
"upgrade" adam to forked "0.20.0"

#581 ryan-williams closed 8 years ago
8
rm "-fasta" from reference-param name

#580 ryan-williams closed 8 years ago
4
Scripts overhaul

#579 ryan-williams closed 8 years ago
6
Merge master into hbupgrade, resolving conflicts, and add a couple things

#578 ryan-williams closed 8 years ago
3
Move commons-io back to standard dep

#577 arahuja closed 8 years ago
1
add somatic-standard end-to-end test

#576 ryan-williams closed 8 years ago
4
Fix ordering of tumor and normal read data

#575 arahuja closed 8 years ago
6
likelihood nits

#574 ryan-williams closed 8 years ago
2
logging nits

#573 ryan-williams closed 8 years ago
1
throwed exception: ./scripts/guacamole: line 39 :exec: time: not found

#572 car2008 opened 8 years ago
27
Update likelihood code to handle non-uniform allelic mixtures

#571 arahuja closed 8 years ago
4
Move logging to grizzled slf4j

#570 arahuja closed 8 years ago
3
Upgrade Hadoop BAM for better interval filtering

#569 arahuja closed 8 years ago
7
Move likelihood code to breeze

#568 arahuja closed 8 years ago
19