Ecosyste.ms: Issues

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

GitHub / biogo/hts issues and pull requests

#164 - ci: bump go versions

Pull Request - State: closed - Opened by kortschak over 2 years ago

#163 - bgzf: fix test with go1.19

Pull Request - State: closed - Opened by zhsj over 2 years ago - 1 comment

#162 - travis: update go version

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

#161 - bam: do not share buffer with qual between reads

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

#160 - bgzf: fix caching bug in Reader.Seek()

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

#159 - bgzf: Seek() loads wrong block due to readahead caching bug

Issue - State: closed - Opened by csw over 3 years ago - 2 comments

#158 - bgzf: satisfy io.ByteReader

Pull Request - State: closed - Opened by kortschak over 3 years ago - 1 comment

#157 - bam: use heuristics to reduce reallocation

Pull Request - State: closed - Opened by kortschak over 3 years ago - 1 comment

#156 - internal/pool: add a buffer pool and use it

Pull Request - State: closed - Opened by kortschak over 3 years ago - 1 comment

#155 - bgzf: Added check to avoid nil pointer dereference panic when seeking

Pull Request - State: closed - Opened by AlanRace almost 4 years ago - 9 comments

#154 - sam: keep otherTags when adding a duplicate reference on BAM read

Pull Request - State: open - Opened by ckingsford almost 4 years ago - 3 comments

#153 - modules,travis: update for go1.15

Pull Request - State: closed - Opened by kortschak about 4 years ago

#152 - bam: iterate over file when no chunks are given

Pull Request - State: closed - Opened by brentp over 4 years ago

#151 - fai: recognise tab as field separator as well

Pull Request - State: closed - Opened by kortschak over 4 years ago

#150 - fai: add index construction function

Pull Request - State: closed - Opened by kortschak over 4 years ago

#149 - FUNDING: set up sponsorship button

Pull Request - State: closed - Opened by kortschak over 4 years ago - 1 comment

#148 - fai: implement FAI reading and faidx use

Pull Request - State: closed - Opened by kortschak about 5 years ago - 3 comments

#147 - Different performance after 2 launches

Issue - State: open - Opened by jpofmars about 5 years ago - 1 comment

#146 - bam: prevent -1 becoming positive in conversion to int

Pull Request - State: closed - Opened by kortschak about 5 years ago

#145 - bam: Invalid pos for unmapped SAM record

Issue - State: closed - Opened by mnsmar about 5 years ago - 5 comments

#144 - docs: add CONTRIBUTING.md

Pull Request - State: closed - Opened by kortschak about 5 years ago - 1 comment

#143 - sam: simplify docs

Pull Request - State: closed - Opened by kortschak about 5 years ago

#142 - Community

Pull Request - State: closed - Opened by kortschak about 5 years ago

#141 - travis: update for go1.13

Pull Request - State: closed - Opened by kortschak about 5 years ago

#140 - modules: add go.mod and go.sum

Pull Request - State: closed - Opened by kortschak about 5 years ago

#139 - Record.Qual error

Issue - State: closed - Opened by seqyuan about 5 years ago - 1 comment

#138 - Is the 9827_2%2349.bam file still available?

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

#137 - Failure to read reference stats from index

Issue - State: closed - Opened by bsipos over 5 years ago - 3 comments

#136 - Added NewRecordFromAln for building SAM records from "raw" local alignments.

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

#135 - sam: don't compare query length to template length in validation

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

#134 - bam: fix qual encoding length for nil qualities

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

#133 - Possible issue with SAM record validation

Issue - State: closed - Opened by bsipos over 5 years ago - 3 comments

#132 - Fixed record length calculation in BAM writer when qualities are absent.

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

#131 - travis: add recent go versions

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

#130 - cram: add package for building cram support on

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

#129 - bam: Use libdeflate instead of the standard compress/{gzip,flate}

Pull Request - State: closed - Opened by yasushi-saito about 6 years ago - 8 comments

#128 - hts: Address unchecked-error warnings

Pull Request - State: closed - Opened by yasushi-saito about 6 years ago - 3 comments

#127 - Bam reader error on date format (different format)

Issue - State: closed - Opened by ns3116 over 6 years ago - 6 comments

#126 - sam: handle CIGAR operations longer than 1<<28-1 more gracefully

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

#125 - bam: fix attempt to get name from nil *os.File

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

#124 - Faster bgzf compression/decompression with libdeflate?

Issue - State: open - Opened by chrchang over 6 years ago - 2 comments

#123 - header parsing error with CL.

Issue - State: closed - Opened by brentp over 6 years ago - 13 comments

#122 - Add methods to sam.Seq to get the N'th base without expanding.

Pull Request - State: closed - Opened by yasushi-saito almost 7 years ago - 1 comment

#121 - csi: don't break early when selecting chunks

Pull Request - State: closed - Opened by brentp almost 7 years ago - 1 comment

#120 - bam: add API for controlling merge strategy used by Index

Pull Request - State: closed - Opened by kortschak almost 7 years ago - 2 comments

#119 - Add GetAllOffsets() to retrieve block offsets from a BAM index

Pull Request - State: closed - Opened by yipal almost 7 years ago - 9 comments

#118 - csi,internal: fix stats dummy number handling

Pull Request - State: closed - Opened by kortschak about 7 years ago - 2 comments

#117 - csi: don't break too early when adding chunks

Pull Request - State: closed - Opened by brentp about 7 years ago - 3 comments

#116 - csi: missing chunks from CSI index

Issue - State: closed - Opened by brentp about 7 years ago - 9 comments

#115 - csi: malformed dummy bin header

Issue - State: closed - Opened by brentp about 7 years ago - 10 comments

#114 - bam: fix yet more bounds checks

Pull Request - State: closed - Opened by kortschak over 7 years ago - 3 comments

#113 - bam: fix various bounds checks

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

#112 - bam: make bad auxtags and sequence lengths safe

Pull Request - State: closed - Opened by kortschak over 7 years ago - 1 comment

#111 - bam: reader over allocates in some cases

Issue - State: open - Opened by kortschak over 7 years ago

#110 - bam,sam: fix zero and negativish value handling

Pull Request - State: closed - Opened by kortschak over 7 years ago - 3 comments

#109 - bgzf: fix block size handling errors

Pull Request - State: closed - Opened by kortschak over 7 years ago - 2 comments

#108 - Added fuzz testing for bgzf and bam readers.

Pull Request - State: closed - Opened by yasushi-saito over 7 years ago - 2 comments

#107 - sam: extend support range for ISO8601

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

#106 - iso8601

Issue - State: closed - Opened by brentp over 7 years ago - 4 comments

#105 - sam: make zero length CIGAR or unmapped reads have unit length

Pull Request - State: closed - Opened by kortschak over 7 years ago - 3 comments

#104 - Zero length bam records have invalid bin values

Issue - State: closed - Opened by yipal over 7 years ago - 5 comments

#103 - sam: reflect the behaviour of other tools

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

#102 - sam: fix bin calculation for unmapped reads with mapped mates

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

#101 - Invalid .bam output using hts.bam.Writer

Issue - State: closed - Opened by yipal over 7 years ago - 20 comments

#100 - sam: conform more closely to ISO8601

Pull Request - State: closed - Opened by kortschak over 7 years ago - 1 comment

#99 - Bam reader error on date format

Issue - State: closed - Opened by defgenx over 7 years ago - 3 comments

#98 - bgzf: set default OS to unknown

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

#97 - bgzf: make Close wait on worker completion

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

#96 - bgzf: race?

Issue - State: closed - Opened by brentp almost 8 years ago - 6 comments

#95 - bam: fix merger for short bams

Pull Request - State: closed - Opened by kortschak almost 8 years ago - 1 comment

#94 - The merge process panics when the bam is small

Issue - State: closed - Opened by dongweigogo almost 8 years ago - 1 comment

#93 - bam: add example for paired end deduplication sorting

Issue - State: open - Opened by kortschak almost 8 years ago - 1 comment

#92 - sam: pre-allocate AuxFields

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

#91 - bam,sam: add merging functions

Pull Request - State: closed - Opened by kortschak almost 8 years ago - 2 comments

#90 - sam: optimize ParseAux

Pull Request - State: closed - Opened by brentp almost 8 years ago - 2 comments

#89 - sam: add Omit method to Reader

Issue - State: closed - Opened by brentp almost 8 years ago - 5 comments

#88 - sam: fix CIGAR sequence length validation

Issue - State: closed - Opened by brentp almost 8 years ago

#87 - README: fix markdown

Pull Request - State: closed - Opened by kortschak almost 8 years ago - 1 comment

#86 - sam: fix CIGAR sequence length validation

Pull Request - State: closed - Opened by brentp almost 8 years ago - 2 comments

#85 - sam: fix ownership maintainance during Header cloning

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

#84 - I'm not sure if the record.End() returns thre right position.

Issue - State: closed - Opened by dongweigogo almost 8 years ago - 2 comments

#83 - sam: allow Reference, ReadGroup and Program renames

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

#82 - sam: renaming references, read groups and programs

Issue - State: closed - Opened by kortschak almost 8 years ago - 2 comments

#81 - sam: loosen reference identity check for unlinked refs

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

#79 - sam: update tags list and docs

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

#78 - sam: update aux tags list to match SAM tags document

Issue - State: closed - Opened by kortschak almost 8 years ago - 1 comment

#77 - bam: add Merge function

Issue - State: closed - Opened by dongweigogo almost 8 years ago - 8 comments

#76 - sam: make zero value for Header UnmarshalText without panicking

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

#74 - tabix: replace Read with io.ReadFull

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

#73 - CSI Magic Number

Issue - State: closed - Opened by nathanhaigh almost 8 years ago - 1 comment

#72 - intial CRAM proposal

Pull Request - State: closed - Opened by brentp almost 8 years ago - 5 comments

#71 - paper: properly mark up references

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

#70 - paper/examples/flagstat: add multithreaded samtools

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

#69 - paper/examples/flagstat/README.md misleading?

Issue - State: closed - Opened by sb10 about 8 years ago - 9 comments

#68 - README: add summary, example and community guidelines

Pull Request - State: closed - Opened by kortschak about 8 years ago - 2 comments

#60 - publish: add JOSS paper and metadata

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

#57 - bgzf output not compatible with htslib

Issue - State: closed - Opened by brentp about 8 years ago - 8 comments

#54 - cram support

Issue - State: open - Opened by brentp about 8 years ago - 32 comments