Ecosyste.ms: Issues

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GitHub / inodb/sufam issues and pull requests

#26 - Bump numpy from 1.9.2 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#25 - Bump numpy from 1.9.2 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#24 - ensure FORMAT column is in vcf output (even if excluded from input vcf)

Pull Request - State: open - Opened by raylim over 7 years ago

#23 - vcf AD INFO fields should have a number=R

Pull Request - State: closed - Opened by raylim over 7 years ago

#22 - Give warning for biallelic variants

Issue - State: open - Opened by inodb almost 8 years ago
Labels: enhancement

#21 - Add warning for unknown chromosome/contig

Issue - State: open - Opened by inodb almost 8 years ago
Labels: enhancement

#20 - fix vcf output; add option for chr reference file

Pull Request - State: closed - Opened by raylim almost 8 years ago

#19 - fix vcf output; add option for chr reference file

Pull Request - State: closed - Opened by raylim almost 8 years ago

#18 - Add VCF output and pyvcf dependency

Pull Request - State: closed - Opened by inodb almost 8 years ago
Labels: enhancement

#17 - Check number of records outputted

Issue - State: open - Opened by inodb almost 9 years ago
Labels: enhancement

#16 - Add VCF output format

Issue - State: open - Opened by inodb almost 9 years ago
Labels: enhancement

#15 - Error on unkown reference

Issue - State: open - Opened by inodb almost 9 years ago

#14 - samtools depth is higher than cov column of mpileup

Issue - State: closed - Opened by inodb almost 9 years ago - 1 comment

#13 - Add option to set parameters for mpileup

Issue - State: closed - Opened by inodb almost 9 years ago - 1 comment
Labels: enhancement

#12 - Crash on position with 0 cov if region does contain cov

Issue - State: closed - Opened by inodb about 9 years ago

#11 - Can't handle N in reference

Issue - State: closed - Opened by inodb about 9 years ago - 1 comment

#10 - Sometimes * column is nan instead of 0

Issue - State: open - Opened by inodb over 9 years ago
Labels: bug, enhancement

#9 - add --version option to script

Issue - State: closed - Opened by inodb over 9 years ago

#8 - Initial commit revertant mutation checker

Pull Request - State: closed - Opened by inodb over 9 years ago - 1 comment

#7 - Check indel type and add tests

Pull Request - State: closed - Opened by inodb over 9 years ago

#6 - Revamp

Pull Request - State: closed - Opened by raylim over 9 years ago - 1 comment

#5 - complete revamp of sufam

Pull Request - State: closed - Opened by raylim over 9 years ago - 1 comment

#4 - fix deletions being set as the correct type

Pull Request - State: closed - Opened by raylim over 9 years ago - 1 comment

#3 - fix indels of double digit length

Pull Request - State: closed - Opened by raylim over 9 years ago

#2 - Add two columns for validation

Issue - State: closed - Opened by inodb over 9 years ago

#1 - Include small test set in repo

Issue - State: closed - Opened by inodb over 9 years ago