bigdatagenomics/quinine issues and pull requests

#46 - Scoverage plugin not used properly

Issue - State: open - Opened by gslowikowski almost 8 years ago

#45 - [QUININE-44] Use mate alignment pos instead of alignment end.

Pull Request - State: closed - Opened by fnothaft about 8 years ago - 1 comment

#45 - [QUININE-44] Use mate alignment pos instead of alignment end.

Pull Request - State: closed - Opened by fnothaft about 8 years ago - 1 comment

#44 - Check if mate is aligned before creating mate ReferenceRegion

Issue - State: closed - Opened by fnothaft about 8 years ago
Labels: bug

#44 - Check if mate is aligned before creating mate ReferenceRegion

Issue - State: closed - Opened by fnothaft about 8 years ago
Labels: bug

#43 - [QUININE-42] Catch string index out of range in VariantSite join.

Pull Request - State: closed - Opened by fnothaft about 8 years ago - 1 comment

#42 - String index out of range in ContaminationEstimator/VariantSite

Issue - State: closed - Opened by fnothaft about 8 years ago
Labels: bug

#42 - String index out of range in ContaminationEstimator/VariantSite

Issue - State: closed - Opened by fnothaft about 8 years ago
Labels: bug

#42 - String index out of range in ContaminationEstimator/VariantSite

Issue - State: closed - Opened by fnothaft about 8 years ago
Labels: bug

#42 - String index out of range in ContaminationEstimator/VariantSite

Issue - State: closed - Opened by fnothaft about 8 years ago
Labels: bug

#41 - Add Sequence Ontology identifiers as supported featureTypes

Pull Request - State: closed - Opened by heuermh about 8 years ago - 8 comments

#40 - Add Sequence Ontology identifiers as supported featureTypes

Issue - State: closed - Opened by heuermh over 8 years ago

#40 - Add Sequence Ontology identifiers as supported featureTypes

Issue - State: closed - Opened by heuermh over 8 years ago

#39 - Use flanking instead of startEnd

Issue - State: open - Opened by heuermh over 8 years ago

#39 - Use flanking instead of startEnd

Issue - State: open - Opened by heuermh over 8 years ago

#39 - Use flanking instead of startEnd

Issue - State: open - Opened by heuermh over 8 years ago

#39 - Use flanking instead of startEnd

Issue - State: open - Opened by heuermh over 8 years ago

#38 - [QUININE-11] Compute insert size distribution.

Pull Request - State: open - Opened by fnothaft over 8 years ago - 4 comments

#38 - [QUININE-11] Compute insert size distribution.

Pull Request - State: open - Opened by fnothaft over 8 years ago - 4 comments

#38 - [QUININE-11] Compute insert size distribution.

Pull Request - State: open - Opened by fnothaft over 8 years ago - 4 comments

#38 - [QUININE-11] Compute insert size distribution.

Pull Request - State: open - Opened by fnothaft over 8 years ago - 4 comments

#38 - [QUININE-11] Compute insert size distribution.

Pull Request - State: open - Opened by fnothaft over 8 years ago - 4 comments

#37 - Upgrade to ADAM 0.20.0

Issue - State: open - Opened by fnothaft over 8 years ago

#37 - Upgrade to ADAM 0.20.0

Issue - State: open - Opened by fnothaft over 8 years ago

#37 - Upgrade to ADAM 0.20.0

Issue - State: open - Opened by fnothaft over 8 years ago

#37 - Upgrade to ADAM 0.20.0

Issue - State: open - Opened by fnothaft over 8 years ago

#36 - Misc contamination fixes

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#36 - Misc contamination fixes

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#36 - Misc contamination fixes

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#36 - Misc contamination fixes

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#35 - Join on variant in contamination estimator is flaky

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#35 - Join on variant in contamination estimator is flaky

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#34 - Load allele frequencies from annotated VCFs

Issue - State: closed - Opened by fnothaft over 8 years ago

#34 - Load allele frequencies from annotated VCFs

Issue - State: closed - Opened by fnothaft over 8 years ago

#34 - Load allele frequencies from annotated VCFs

Issue - State: closed - Opened by fnothaft over 8 years ago

#33 - [QUININE-31] Check for non-empty RDD in contamination estimator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#33 - [QUININE-31] Check for non-empty RDD in contamination estimator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#32 - [QUININE-30] Filter out unmapped reads before Join in ContaminationEstimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#32 - [QUININE-30] Filter out unmapped reads before Join in ContaminationEstimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#31 - Check collection size in contamination estimator before running

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: enhancement

#31 - Check collection size in contamination estimator before running

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: enhancement

#31 - Check collection size in contamination estimator before running

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: enhancement

#31 - Check collection size in contamination estimator before running

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: enhancement

#31 - Check collection size in contamination estimator before running

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: enhancement

#30 - Filter out unmapped reads before running Region Joins

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#30 - Filter out unmapped reads before running Region Joins

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#30 - Filter out unmapped reads before running Region Joins

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#30 - Filter out unmapped reads before running Region Joins

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#29 - [QUININE-28] Fix contamination estimator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#29 - [QUININE-28] Fix contamination estimator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#29 - [QUININE-28] Fix contamination estimator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#29 - [QUININE-28] Fix contamination estimator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#28 - Contamination estimator can fail if 95% window is too small

Issue - State: closed - Opened by fnothaft over 8 years ago - 1 comment
Labels: bug

#28 - Contamination estimator can fail if 95% window is too small

Issue - State: closed - Opened by fnothaft over 8 years ago - 1 comment
Labels: bug

#28 - Contamination estimator can fail if 95% window is too small

Issue - State: closed - Opened by fnothaft over 8 years ago - 1 comment
Labels: bug

#28 - Contamination estimator can fail if 95% window is too small

Issue - State: closed - Opened by fnothaft over 8 years ago - 1 comment
Labels: bug

#27 - [QUININE-26] Check for empty distribution before computing median.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#27 - [QUININE-26] Check for empty distribution before computing median.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#26 - `CoverageStats` trips assert if distribution is empty

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#26 - `CoverageStats` trips assert if distribution is empty

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#25 - [QUININE-24] Fix NPE in ReadStats.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#25 - [QUININE-24] Fix NPE in ReadStats.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#24 - ReadStats NPE's on reads with null qualities

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#24 - ReadStats NPE's on reads with null qualities

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug

#23 - Refactor main to delegate to ADAMMain

Pull Request - State: open - Opened by heuermh over 8 years ago - 8 comments

#23 - Refactor main to delegate to ADAMMain

Pull Request - State: open - Opened by heuermh over 8 years ago - 8 comments

#22 - Add RNA-seq tool

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 4 comments

#22 - Add RNA-seq tool

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 4 comments

#21 - [QUININE-20] Adding allele frequency annotator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#21 - [QUININE-20] Adding allele frequency annotator.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#20 - Add MAF annotator

Issue - State: closed - Opened by fnothaft over 8 years ago

#20 - Add MAF annotator

Issue - State: closed - Opened by fnothaft over 8 years ago

#20 - Add MAF annotator

Issue - State: closed - Opened by fnothaft over 8 years ago

#19 - Add contamination estimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#19 - Add contamination estimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#19 - Add contamination estimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#19 - Add contamination estimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#19 - Add contamination estimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#19 - Add contamination estimator

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 6 comments

#18 - Targeted sequencing panel metrics

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#18 - Targeted sequencing panel metrics

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#18 - Targeted sequencing panel metrics

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#18 - Targeted sequencing panel metrics

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 2 comments

#17 - Add RNA-seq QC tool

Issue - State: closed - Opened by fnothaft over 8 years ago

#17 - Add RNA-seq QC tool

Issue - State: closed - Opened by fnothaft over 8 years ago

#16 - Add sample contamination estimator

Issue - State: closed - Opened by fnothaft over 8 years ago

#16 - Add sample contamination estimator

Issue - State: closed - Opened by fnothaft over 8 years ago

#16 - Add sample contamination estimator

Issue - State: closed - Opened by fnothaft over 8 years ago

#16 - Add sample contamination estimator

Issue - State: closed - Opened by fnothaft over 8 years ago

#16 - Add sample contamination estimator

Issue - State: closed - Opened by fnothaft over 8 years ago

#16 - Add sample contamination estimator

Issue - State: closed - Opened by fnothaft over 8 years ago

#15 - Add in metrics for targeted sequencing panels

Issue - State: closed - Opened by fnothaft over 8 years ago

#15 - Add in metrics for targeted sequencing panels

Issue - State: closed - Opened by fnothaft over 8 years ago

#15 - Add in metrics for targeted sequencing panels

Issue - State: closed - Opened by fnothaft over 8 years ago

#14 - Compute coverage distribution

Issue - State: closed - Opened by fnothaft over 8 years ago

#14 - Compute coverage distribution

Issue - State: closed - Opened by fnothaft over 8 years ago

#14 - Compute coverage distribution

Issue - State: closed - Opened by fnothaft over 8 years ago

#13 - Re-renaming project.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#13 - Re-renaming project.

Pull Request - State: closed - Opened by fnothaft over 8 years ago - 3 comments

#12 - Vote of no confidence in new repository name

Issue - State: closed - Opened by heuermh over 8 years ago

GitHub / bigdatagenomics/quinine issues and pull requests