github.com/BioJulia/XAM.jl issues | Ecosyste.ms: OpenCollective

Support for Concurrent Access with XAM.jl: Reader/Writer Safety and Locking Considerations

abhinavsns opened this issue 2 months ago

Read sequences don't have overlapping with gene, but eachoverlap() reported there're.

Xiao-Zhong opened this issue 2 months ago

CompatHelper: bump compat for TranscodingStreams to 0.11, (keep existing compat)

github-actions[bot] opened this pull request 4 months ago

Has flag() renamed to flags()?

egoecho opened this issue 5 months ago

error when using SAM.auxdata(record)

yr-neurospace opened this issue 6 months ago

Do not allow unused trailing bytes in BAM records

jakobnissen opened this pull request 7 months ago

Rewrite BAM auxiliary data

jakobnissen opened this pull request 7 months ago

CompatHelper: bump compat for GenomicFeatures to 3, (keep existing compat)

github-actions[bot] opened this pull request 9 months ago

CompatHelper: bump compat for Indexes to 0.2, (keep existing compat)

github-actions[bot] opened this pull request 9 months ago

Correct YML whitespace

CiaranOMara opened this pull request 9 months ago

Release/v0.4.0

CiaranOMara opened this pull request 9 months ago

XAM compatibilty for Automa very old, please update?

mashu opened this issue 9 months ago

add conversion from SAM to BAM

jonathanBieler opened this pull request over 1 year ago

Fix deprecated find in header docs

jonathanBieler opened this pull request over 1 year ago

[WIP] convert SAM to BAM

jonathanBieler opened this issue over 1 year ago

while loop got eof error

junjunlab opened this issue over 1 year ago

Add eachoverlap(reader::Reader, refname::String)

apraga opened this issue over 1 year ago

Correct way to add records to an array

krishvishal opened this issue almost 2 years ago

Release 0.3.1

MillironX opened this pull request about 2 years ago

added method for handling different bam index types

jonathanBieler opened this pull request about 2 years ago

Upgrade to BioAlignments v3

MillironX opened this pull request about 2 years ago

Switch to Oneflow

MillironX opened this issue about 2 years ago

Release v0.3.0

MillironX opened this pull request about 2 years ago

Do you have the plan to add the pileup functions?

panxiaoguang opened this issue about 2 years ago

hotfix/issue 31

CiaranOMara opened this pull request about 2 years ago

Add `index!(reader::Reader, path)`

CiaranOMara opened this issue about 2 years ago

Upgrade BioAlignments to v2.2 & BioSequences to v3

MillironX opened this pull request over 2 years ago

Finding a map between observed bases and positions in the reference genome

scikal opened this issue over 2 years ago

Feature Request: Conversion from `BioAlignments` to `SAM.Record`

MillironX opened this issue almost 3 years ago

how to use @threads to use multithreads when reading BAM file

panxiaoguang opened this issue almost 3 years ago

Improve documentation of flag function

jakobnissen opened this pull request almost 3 years ago

Make `seqname` consistent with BioJulia ecosystem

CiaranOMara opened this issue about 3 years ago

Install ERROR: Unsatisfiable requirements detected for package BioSequences

egoecho opened this issue over 3 years ago

Position of unmapped mate

CiaranOMara opened this issue over 3 years ago

can you add some functions to BAM.Reader?

panxiaoguang opened this issue over 3 years ago

CompatHelper: bump compat for "Indexes" to "0.2"

github-actions[bot] opened this pull request over 3 years ago

CompatHelper: bump compat for "Indexes" to "0.2"

github-actions[bot] opened this pull request over 3 years ago

TagBot trigger issue

JuliaTagBot opened this issue over 3 years ago

Constrain automa upper bound

kescobo opened this pull request over 3 years ago

Broken with Automa 0.8.1

dialvarezs opened this issue over 3 years ago

Browsing the documentation

george-githinji opened this issue over 3 years ago

Switch to CodecBGZF

jakobnissen opened this pull request over 3 years ago

eachoverlap running past end of stream

rulixxx opened this issue almost 4 years ago

BoundsError in eachoverlap()

yuifu opened this issue about 4 years ago

Migrate from BGZFStreams to CodecBGZF

jakobnissen opened this issue about 4 years ago

Begin crosschecks

CiaranOMara opened this pull request about 4 years ago

Rehaul BAM and SAM accessor functions

jakobnissen opened this pull request about 4 years ago

Amend field access errors

jakobnissen opened this pull request about 4 years ago

Make BAM record layout match BAM specs

jakobnissen opened this pull request about 4 years ago

Converge SAM and BAM records

jakobnissen opened this issue about 4 years ago

Various spec violations

jakobnissen opened this issue about 4 years ago

Error when opening a BAM file generated by HISAT2 version 2.2.0

yuifu opened this issue over 4 years ago

Fixes BAM.isnextmapped()

dialvarezs opened this pull request over 4 years ago

release/v0.2.5

CiaranOMara opened this pull request over 4 years ago

hotfix/encode_copy

CiaranOMara opened this pull request over 4 years ago

Fix ambiguity in parser

jakobnissen opened this pull request over 4 years ago

hotfix/iterate

CiaranOMara opened this pull request over 4 years ago

Is there any way to check whether chromosome is available for a BAM file when using eachoverlap()?

yuifu opened this issue over 4 years ago

Memory leak

CiaranOMara opened this issue over 4 years ago

CompatHelper: bump compat for "BioSequences" to "2.0"