Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / AdamaJava/adamajava issues and pull requests

#100 - Create README.md for qannotate

Pull Request - State: closed - Opened by holmeso over 5 years ago - 1 comment

#99 - update qannotate unit test without update sorceCode under src floder

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 2 comments

#97 - Develop.master

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 10 comments

#96 - Create pull_request_template.md

Pull Request - State: closed - Opened by holmeso over 5 years ago - 2 comments
Labels: enhancement

#94 - Fix to ChrPositionComparator - ready for GRCh38

Pull Request - State: closed - Opened by holmeso over 5 years ago

#93 - qannotate is using a hard-coded list of contig names to sort output

Issue - State: closed - Opened by holmeso over 5 years ago
Labels: bug

#91 - adding novaseq and nextseq to the list of platforms that qsv supports

Pull Request - State: closed - Opened by holmeso over 5 years ago

#90 - Qannotate jul2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 11 comments

#89 - Qannotate jul2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 1 comment

#88 - Q3indel vcf header

Pull Request - State: closed - Opened by holmeso over 5 years ago

#87 - q3indel vcf has validation errors

Issue - State: closed - Opened by holmeso over 5 years ago
Labels: enhancement, invalid

#86 - moved vcf header filter descriptions from qsnp to qannotate

Pull Request - State: closed - Opened by holmeso over 5 years ago - 1 comment

#85 - COV vcf header should contain coverage cutoff values used

Issue - State: open - Opened by holmeso over 5 years ago
Labels: enhancement, is anybody here a genome biologist?

#84 - Add entry to vcf header for 5BP

Issue - State: open - Opened by holmeso over 5 years ago - 3 comments
Labels: enhancement, is anybody here a genome biologist?

#83 - Deprecate/delete method that modifies chromosome name

Issue - State: open - Opened by holmeso over 5 years ago - 4 comments
Labels: enhancement

#82 - change to getFullChromosome so that if supplied ref is chrM, that is …

Pull Request - State: closed - Opened by holmeso over 5 years ago - 3 comments

#81 - Qprofiler jul2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#80 - change ambiguous attribute name file_checksum to md5sum.

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#78 - Qprofiler jun2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#77 - readCount for MD error rate

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#76 - Create README.md

Pull Request - State: closed - Opened by grendeloz over 5 years ago - 2 comments

#75 - multi-thread bug fix

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#74 - Qprofiler jun2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#73 - Qprofiler jun2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#72 - bug fix for bams with lots of clipping

Pull Request - State: closed - Opened by holmeso over 5 years ago - 7 comments

#71 - QSV out of memory when run against BAM with lots of clipping

Issue - State: closed - Opened by holmeso over 5 years ago - 1 comment
Labels: bug

#70 - Qprofiler may2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 3 comments

#69 - Qprofiler may2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 1 comment

#68 - Qprofiler may2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 1 comment

#67 - Qprofiler may2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#66 - Qprofiler may2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago

#65 - Qprofiler may2019

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 1 comment

#64 - seperate common code into old qprofiler and qprofiler2

Pull Request - State: closed - Opened by ChristinaXu2017 over 5 years ago - 1 comment

#63 - Add bgi to qsv

Pull Request - State: closed - Opened by holmeso over 5 years ago

#62 - Fixes #61

Pull Request - State: closed - Opened by delocalizer over 5 years ago

#60 - Add MGIseq2000 as a Platform for qSV

Issue - State: closed - Opened by bioInfo25 over 5 years ago - 8 comments
Labels: enhancement

#59 - qsv - minor refactoring

Pull Request - State: closed - Opened by holmeso over 5 years ago

#58 - de-randomise removal of overlapping reads

Pull Request - State: closed - Opened by holmeso over 5 years ago

#57 - Overlap in qsnp

Pull Request - State: closed - Opened by holmeso over 5 years ago

#56 - CreateQsnpIni failing

Issue - State: closed - Opened by shimbalama over 5 years ago - 2 comments

#55 - fix homopolymer bug at start/end of contigs

Pull Request - State: closed - Opened by holmeso over 5 years ago

#54 - qannotate homopolymer mode throws unhelpful exception

Issue - State: closed - Opened by holmeso over 5 years ago - 3 comments
Labels: is anybody here a genome biologist?

#53 - Put the qsnp ini generator into qsnp project

Pull Request - State: closed - Opened by delocalizer over 5 years ago

#52 - Qsnp min threshold

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#51 - add final to immutable string variable

Pull Request - State: closed - Opened by ChristinaXu2017 almost 6 years ago - 1 comment

#50 - Fix static fields in XmlUtils.java

Issue - State: closed - Opened by holmeso almost 6 years ago - 1 comment

#49 - Fix for #48

Pull Request - State: closed - Opened by delocalizer almost 6 years ago - 3 comments

#48 - SignatureGenerator dies with StackOverflow

Issue - State: closed - Opened by delocalizer almost 6 years ago - 3 comments

#47 - Query the values for MIN threshold in qsnp

Issue - State: closed - Opened by delocalizer almost 6 years ago - 4 comments
Labels: is anybody here a genome biologist?

#46 - Qprofiler2 develop

Pull Request - State: closed - Opened by ChristinaXu2017 almost 6 years ago - 2 comments

#45 - Qprofiler2 develop

Pull Request - State: closed - Opened by ChristinaXu2017 almost 6 years ago - 1 comment

#44 - Create CONTRIBUTING.md

Pull Request - State: closed - Opened by holmeso almost 6 years ago - 2 comments

#42 - qprofiler complaining when running against fastqs with long read length (300)

Issue - State: closed - Opened by holmeso almost 6 years ago - 1 comment

#41 - Removing two redundant null checks in GenotypeUtil

Pull Request - State: closed - Opened by MichielDean almost 6 years ago - 1 comment

#40 - Qsv readme

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#39 - adding README to qprofiler project

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#38 - Remove version numbers from jar filenames

Issue - State: closed - Opened by holmeso almost 6 years ago - 1 comment
Labels: enhancement

#37 - Add attributes

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#36 - Revert "removed unnecessary null check of acc in getFormatFilter"

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#35 - removed unnecessary null check of acc in getFormatFilter

Pull Request - State: closed - Opened by sarahk2019 almost 6 years ago - 5 comments

#34 - unnecessary null check

Issue - State: open - Opened by holmeso almost 6 years ago
Labels: bug, good first issue

#33 - Qprofiler2 develop

Pull Request - State: closed - Opened by ChristinaXu2017 almost 6 years ago - 1 comment

#32 - added checkstyle config and gradle plugins for checkstyle and findbugs

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#31 - Add styling and static bug detection to build

Issue - State: closed - Opened by holmeso almost 6 years ago

#30 - Qprofiler2 develop

Pull Request - State: closed - Opened by ChristinaXu2017 almost 6 years ago - 5 comments

#29 - update qcommon, qprofiler readay for new qprofiler2

Pull Request - State: closed - Opened by ChristinaXu2017 almost 6 years ago - 1 comment

#28 - Qprofiler new xml

Pull Request - State: closed - Opened by ChristinaXu2017 almost 6 years ago - 1 comment

#27 - Fix vcf merge bug

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#26 - missing vcf records in nightly (latest) regression

Issue - State: closed - Opened by holmeso almost 6 years ago

#25 - Values from vcf filter fields will now appear in maf

Pull Request - State: closed - Opened by holmeso almost 6 years ago - 3 comments

#24 - Qsnp hangs

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#23 - Fix issues around the AD format field

Pull Request - State: closed - Opened by holmeso almost 6 years ago

#22 - qsnp hangs when bams are sporadically populated

Issue - State: closed - Opened by holmeso almost 6 years ago - 1 comment
Labels: bug

#20 - Logic for calling MNPs in vcf mode is not correct

Issue - State: closed - Opened by delocalizer almost 6 years ago - 3 comments
Labels: bug

#19 - qannotate to fail gracefully should no reference `.dict` file be supplied

Issue - State: closed - Opened by delocalizer about 6 years ago - 2 comments

#18 - Tidy up qannotate Overlap mode

Issue - State: open - Opened by holmeso about 6 years ago

#17 - q3Indel to fail gracefully should no index file be supplied

Issue - State: closed - Opened by holmeso about 6 years ago - 1 comment

#16 - update overlap mode usage

Pull Request - State: closed - Opened by ChristinaXu2017 about 6 years ago

#15 - Add documentation for main page and relevant sub pages

Issue - State: open - Opened by holmeso about 6 years ago - 3 comments

#14 - should be ok

Pull Request - State: closed - Opened by holmeso over 6 years ago

#13 - Add parameters to confidence mode

Pull Request - State: closed - Opened by holmeso over 6 years ago - 1 comment

#11 - Create a wdl workflow that will just run the qannotate ConfidenceMode and MergeVCf MergeMaf.

Issue - State: closed - Opened by holmeso over 6 years ago - 1 comment
Labels: enhancement

#10 - update mainClass on qprofiler2

Pull Request - State: closed - Opened by ChristinaXu2017 over 6 years ago - 1 comment

#9 - Vcf2Maf filter field not being set

Issue - State: closed - Opened by holmeso over 6 years ago

#8 - Adama test

Pull Request - State: closed - Opened by ChristinaXu2017 over 6 years ago - 2 comments

#7 - MergeVcfs is not appropriately updating AD format field

Issue - State: closed - Opened by holmeso over 6 years ago - 1 comment
Labels: bug

#6 - update confidence mode code

Issue - State: closed - Opened by holmeso over 6 years ago - 1 comment

#5 - add getRef and test

Pull Request - State: closed - Opened by holmeso over 6 years ago

#4 - updated to include alt in equals method, added tests

Pull Request - State: closed - Opened by holmeso over 6 years ago - 5 comments

#3 - pull build from lastest sourceforge to git

Pull Request - State: closed - Opened by ChristinaXu2017 over 6 years ago - 1 comment

#2 - remove redundant testing git.build.gradle

Pull Request - State: closed - Opened by CanWood over 6 years ago

#1 - get version id from git

Pull Request - State: closed - Opened by holmeso over 6 years ago - 9 comments