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 5 months ago

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

Xiao-Zhong opened this issue 5 months ago

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

github-actions[bot] opened this pull request 6 months ago

Has flag() renamed to flags()?

egoecho opened this issue 8 months ago

error when using SAM.auxdata(record)

yr-neurospace opened this issue 9 months ago

Do not allow unused trailing bytes in BAM records

jakobnissen opened this pull request 10 months ago

Rewrite BAM auxiliary data

jakobnissen opened this pull request 10 months ago

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

github-actions[bot] opened this pull request 11 months ago

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

github-actions[bot] opened this pull request 11 months ago

Correct YML whitespace

CiaranOMara opened this pull request 11 months ago

Release/v0.4.0

CiaranOMara opened this pull request 12 months ago

XAM compatibilty for Automa very old, please update?

mashu opened this issue 12 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 almost 2 years ago

Correct way to add records to an array

krishvishal opened this issue about 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 over 2 years ago

hotfix/issue 31

CiaranOMara opened this pull request over 2 years ago

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

CiaranOMara opened this issue over 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 about 3 years ago

Improve documentation of flag function

jakobnissen opened this pull request about 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 almost 4 years ago

TagBot trigger issue

JuliaTagBot opened this issue almost 4 years ago

Constrain automa upper bound

kescobo opened this pull request almost 4 years ago

Broken with Automa 0.8.1

dialvarezs opened this issue almost 4 years ago

Browsing the documentation

george-githinji opened this issue almost 4 years ago

Switch to CodecBGZF

jakobnissen opened this pull request almost 4 years ago

eachoverlap running past end of stream

rulixxx opened this issue about 4 years ago

BoundsError in eachoverlap()

yuifu opened this issue over 4 years ago

Migrate from BGZFStreams to CodecBGZF

jakobnissen opened this issue over 4 years ago

Begin crosschecks

CiaranOMara opened this pull request over 4 years ago

Rehaul BAM and SAM accessor functions

jakobnissen opened this pull request over 4 years ago

Amend field access errors

jakobnissen opened this pull request over 4 years ago

Make BAM record layout match BAM specs

jakobnissen opened this pull request over 4 years ago

Converge SAM and BAM records

jakobnissen opened this issue over 4 years ago

Various spec violations

jakobnissen opened this issue over 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"