biodatageeks/sequila issues and pull requests

#180 - Fix comet condition

Pull Request - State: closed - Opened by mwiewior 4 months ago

#179 - feat: First part of Comet fixes

Pull Request - State: closed - Opened by mwiewior 4 months ago

#178 - fix: Spark 3.4.3 cleanup

Pull Request - State: closed - Opened by mwiewior 4 months ago

#177 - fix: IntMap class duplication issue

Pull Request - State: closed - Opened by mwiewior 4 months ago

#176 - fix: Bumping sbtSonatype

Pull Request - State: closed - Opened by mwiewior 4 months ago

#175 - fix: Disable doc generation

Pull Request - State: closed - Opened by mwiewior 4 months ago

#174 - feat: spark 3.4 support

Pull Request - State: closed - Opened by mwiewior 4 months ago

#173 - Feature/ximmer coverage

Pull Request - State: open - Opened by kkobylin almost 2 years ago

#172 - fix:race condition for local[n] in toCoverage method

Pull Request - State: closed - Opened by mwiewior almost 2 years ago

#171 - Handle "bad" contig entries in coverage and pileup (missing keys in contigMap)

Issue - State: closed - Opened by mwiewior almost 2 years ago
Labels: bug

#170 - Spark 3.2.2

Pull Request - State: closed - Opened by mwiewior about 2 years ago

#169 - feat: Additional interval joins implementations

Pull Request - State: open - Opened by mwiewior over 2 years ago

#168 - Add feature_counts function to Spark SQL

Pull Request - State: open - Opened by kkobylin over 2 years ago

#167 - Fix/benchmark fix

Pull Request - State: open - Opened by mwiewior almost 3 years ago

#166 - flagstat v2

Pull Request - State: open - Opened by meibrahim almost 3 years ago

#165 - Benchmarking and page update

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#164 - Interval joins bench migrated

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#163 - Doc/benchmark details

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#162 - Pileup/cov tests supplements

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#161 - update to bench on landing pge

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#160 - Adding google analytics

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#159 - Create FlagStat.

Pull Request - State: closed - Opened by meibrahim almost 3 years ago

#158 - FlagStat

Pull Request - State: closed - Opened by meibrahim almost 3 years ago

#157 - Introduction and Cloud sections

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#156 - Adding support for filtering by mapping quality

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#155 - Python/SQL api

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#154 - Add filtering by mapping qual

Issue - State: closed - Opened by mwiewior almost 3 years ago - 1 comment
Labels: enhancement

#153 - Adding new param page

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#152 - Adding mock benchmark

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#151 - Getting started updates

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#150 - Fixing branch

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#149 - Migrating documentation

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#148 - Adding unit test for saving pileup using Dataframe API without quals

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#147 - Bugfix for qualsMapVector

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#146 - Fixing vectorized write without quals

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#145 - Release with proper JDK 8 support

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#144 - fix badge

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#143 - Fixing partition bounds with index

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#142 - Remove reference parameter from coverage calcs

Issue - State: closed - Opened by mwiewior almost 3 years ago
Labels: enhancement

#141 - Fixing log4j issue

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#140 - Log4j error

Issue - State: closed - Opened by mwiewior almost 3 years ago - 1 comment
Labels: bug

#139 - Fixing merge jars

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#138 - Run benchmarks

Issue - State: open - Opened by mwiewior almost 3 years ago

#137 - Update Readme.md

Issue - State: open - Opened by mwiewior almost 3 years ago
Labels: documentation, enhancement

#136 - Global documentation refactor

Issue - State: closed - Opened by mwiewior almost 3 years ago - 1 comment
Labels: documentation

#135 - Refactor SequilaSession to get rid of SequilaRegister

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#134 - Coverage/pileup DataSet/Dataframe API

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#133 - Different phred encoding

Issue - State: open - Opened by mwiewior about 3 years ago
Labels: enhancement

#132 - Add configuration glossary

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: documentation

#131 - Pileup vectorized

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#130 - Pacbio fixes

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#129 - Prepare a pysequila package update for a new release

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: enhancement

#128 - Migrate CI/CD to github actions

Issue - State: open - Opened by mwiewior about 3 years ago
Labels: enhancement

#127 - Add landing page with simple hello wordl scala/python

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment

#126 - Add condition to ctas/save to use vectorized write when pileup method is used

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: bug, invalid

#125 - Add vectorized writer for pileup when saved to ORC

Issue - State: closed - Opened by mwiewior about 3 years ago

#124 - hasDelOnPosition fix

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#123 - Vectorized ORC Writer for Coverage

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#122 - Fix/oob long reads

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#121 - Fixing parquet output for coverage

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#120 - Perf/cov optim

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#119 - Feat/cov no ref

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#118 - Parquet/CSV save methods do not work - ORC does

Issue - State: closed - Opened by mwiewior about 3 years ago - 2 comments
Labels: bug

#117 - Coverage performance tuning

Issue - State: open - Opened by mwiewior about 3 years ago
Labels: enhancement, performance

#116 - common relative pos

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#115 - changed dels and inserts representation from set to list

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#114 - Investiate how to optimize CRAM index access without using reference if only contig and positions needed

Issue - State: open - Opened by mwiewior about 3 years ago
Labels: enhancement, question, performance

#113 - OOB from relativePos (101)

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: bug, wgs

#112 - Quality OOB with long reads

Issue - State: closed - Opened by mwiewior about 3 years ago - 2 comments
Labels: bug, long reads

#111 - Slow performance of long reads

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: bug, long reads

#110 - Various WGS and long reads fixes

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#109 - Bug in gupta

Issue - State: closed - Opened by mwiewior about 3 years ago - 2 comments

#108 - Issue with empty iterator on some partitions - add check on iterator and filtering nulls

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: bug

#107 - Optimize getPartitionLowerBound to return only contig, start and stop - not whole reads

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: enhancement

#106 - Fixing cram support

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#105 - Fixing CRAM tests

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#104 - Feat/ints vs shorts

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#103 - Silent and GKL by default

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#102 - Feature/hashmap intmap

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#101 - Perf/hasdeletion

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#100 - lazy cigar conf

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#99 - ValidationStringency.SILENT as default

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: bug

#98 - Fix/clean contig

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#97 - Pileup regression

Issue - State: closed - Opened by mwiewior about 3 years ago - 1 comment
Labels: bug, performance

#96 - extended rstree buffer

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#95 - Feature/quals buffer

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#94 - Perf/fast inserts

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#93 - quals structure changed to composite key map

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#92 - quals as 3d array

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#91 - Feat/smarter quals allocation

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#90 - Fix/quals optim ctd

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#89 - Pileup cleanup

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#86 - Removed disq hardcode

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#85 - removed break

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#81 - Feat/cov out

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#80 - Fix/quals optim

Pull Request - State: closed - Opened by agaszmurlo about 3 years ago

#77 - RangePartitioner

Pull Request - State: closed - Opened by mwiewior about 3 years ago

#71 - Changing BaseIntervalHolder to abstract class

Pull Request - State: closed - Opened by mwiewior over 3 years ago

#70 - Docs/pluggable intervaljoin

Pull Request - State: open - Opened by tgambin over 3 years ago

#51 - Bump disq to 0.3.6 and htsjdk 2.21 for better CRAM support

Issue - State: closed - Opened by mwiewior almost 4 years ago - 1 comment

GitHub / biodatageeks/sequila issues and pull requests