broadinstitute gatk-dataflow issues

broadinstitute / gatk-dataflow

Development dataflow

BSD 3-Clause "New" or "Revised" License

4 stars 1 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Tw local base recalibrator test

#41 lbergelson opened 9 years ago
0
Support reading VCF files from Hadoop.

#40 lbergelson opened 9 years ago
0
insertSizeMetrics

#39 lbergelson opened 9 years ago
0
GenericJson.clone() method blows up when trying to clone Google reads

#38 akiezun opened 9 years ago
12
Investigate groupbykey OOM.

#37 akiezun opened 9 years ago
1
Fix java.lang.VerifyError: Bad type on operand stack

#36 akiezun opened 9 years ago
6
Make a generic version of overalapping intervals

#35 akiezun opened 9 years ago
0
Sharded Variant Reader

#34 akiezun opened 9 years ago
2
Figure out best way to combine data for "nearby" intervals in dataflow

#33 akiezun opened 9 years ago
3
Write common interfaces for the different kinds of transforms we identify in the dataflow read pre-processing pipeline

#32 akiezun opened 9 years ago
1
Write a helper to quickly go from function -> PTransform.

#31 akiezun opened 9 years ago
8
Extract CoordinateOrder from MarkDuplicatesDataflow.java and unify with other comparators

#30 akiezun opened 9 years ago
0
Fix the warning about Vfs.dir when registering genomics coders

#29 akiezun opened 9 years ago
0
Support writing large BAM files in dataflow

#28 akiezun opened 9 years ago
4
Optimize RemoveDuplicateReadVariantPairs

#27 akiezun opened 9 years ago
0
Refactor Dataflow transforms by "top level" transform

#26 akiezun opened 9 years ago
0
Name Dataflow pipelines

#25 akiezun opened 9 years ago
0
Profile and optimize the ReadsPreprocessingPipeline

#24 akiezun opened 9 years ago
1
Provide a mechanism for dataflow authentication information to be set once and stay set

#23 akiezun opened 9 years ago
0
Consider replacing ReferenceShard and VariantShard with SimpleInterval

#22 akiezun opened 9 years ago
0
Implement temporary way to write large BAM output in dataflow

#21 akiezun opened 9 years ago
1
Determine how to deal with immutability requirement / sibling fusion in dataflow

#20 akiezun opened 9 years ago
6
Fix all dataflow tests and make them mandatory.

#19 akiezun opened 9 years ago
4
Choose approach to fix scaling of ReadBAMTransform, and implement fix

#18 akiezun opened 9 years ago
3
Fix and reenable testGetInvalidPCollectionLocal()

#17 akiezun opened 9 years ago
0
KeyVariantsByRead.key removes reads that don't have variants

#16 akiezun opened 9 years ago
2
Dataflow BQSR Direct Runner fails with --knownSites

#15 akiezun opened 9 years ago
0
Profile options for passing reference data to workers in dataflow

#14 akiezun opened 9 years ago
2
Allow common dataflow options to be specified via a config file

#13 akiezun opened 9 years ago
3
ReadBAMTransform.getReadsFromBAMFilesSharded() is flawed

#12 akiezun opened 9 years ago
3
Create utility method to get Genomics credential given a ProcessContext

#11 akiezun opened 9 years ago
0
Add mechanism to generate unique ids for data types (reads, variants, etc.)

#10 akiezun opened 9 years ago
0
use SmallBamWriter in dataflow tests

#9 akiezun opened 9 years ago
0
Make it easier for test authors to make their tests toggle-able between different dataflow backends

#8 akiezun opened 9 years ago
0
Extract facility for cloud dataflow runs to create local output.

#7 akiezun opened 9 years ago
0
Support interval input in dataflow read pre-processing pipeline

#6 akiezun opened 9 years ago
2
migrate code from googlegenomics/genomics-pipeline

#5 akiezun opened 9 years ago
0
implement ApplyBQSR on dataflow

#4 akiezun opened 9 years ago
4
write a custom source for bam files

#3 akiezun opened 9 years ago
2
Consider using com.google.cloud.dataflow.sdk.transforms.Partition<T> for read/variant filtering

#2 akiezun opened 9 years ago
0
Investigate dataflow debugging/error logging

#1 akiezun opened 9 years ago
1