Ecosyste.ms: Issues

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

GitHub / brentp/hts-nim issues and pull requests

#87 - Adjust header on load to prevent failing [QUESTION]

Issue - State: open - Opened by edg1983 2 months ago - 1 comment

#86 - Closing BGZI gives a 'munmap_chunk(): invalid pointer'

Issue - State: open - Opened by xbello 9 months ago - 3 comments

#85 - slimmer image from Dockerfile

Pull Request - State: closed - Opened by rulixxx about 1 year ago - 3 comments

#84 - Question: changing BAM alignment records in place

Issue - State: closed - Opened by andreas-wilm almost 2 years ago - 4 comments

#83 - remove shallow for ARC/ORC

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

#82 - Question about multiple nalts for single record

Issue - State: closed - Opened by KyleStiers about 2 years ago - 4 comments

#81 - Added bcf_index_build3 support to generate index files for bcf + vcf

Pull Request - State: closed - Opened by ayman-albaz over 2 years ago - 2 comments

#80 - remove deadCodeElim statement

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

#79 - Trouble with newRecord "undeclared identifier" in bam

Issue - State: open - Opened by akkellogg almost 3 years ago - 7 comments

#78 - Issues with nimble test

Issue - State: closed - Opened by lucia-ramirez about 3 years ago - 6 comments

#77 - Modifying GT from ivcf and write to ovcf for multiple pairs of inputs and outputs

Issue - State: closed - Opened by ruqianl about 3 years ago - 6 comments

#76 - Is there any way to get the variant's row index when using the iterator query()

Issue - State: closed - Opened by ruqianl about 3 years ago - 2 comments

#75 - Swapped the order of tid and mate_tid

Pull Request - State: closed - Opened by kojix2 over 3 years ago

#74 - Get list of INFO and FORMAT keys from Header

Issue - State: open - Opened by edg1983 over 3 years ago - 1 comment

#73 - Error: unhandled exception: invalid bgzf file [ValueError]

Issue - State: open - Opened by Stikus over 3 years ago

#72 - Static build with libRmath-nim library causing undefined reference

Issue - State: closed - Opened by ruqianl almost 4 years ago - 3 comments

#71 - Version tag in 0.3.13 is wrong

Issue - State: closed - Opened by Benjamin-Lee almost 4 years ago - 1 comment

#70 - No public facing method for closing Fai file

Issue - State: closed - Opened by NatPRoach almost 4 years ago - 3 comments

#69 - Failure to compile when using new Nim Gas (ORC and ARC)

Issue - State: closed - Opened by Benjamin-Lee almost 4 years ago - 2 comments

#68 - fix `csize_t` for Nim 1.0.x

Pull Request - State: closed - Opened by narimiran about 4 years ago - 1 comment

#67 - Warnings

Pull Request - State: closed - Opened by pb-cdunn about 4 years ago - 2 comments

#66 - Static binary not working from AMD nodes

Issue - State: open - Opened by telatin about 4 years ago - 6 comments

#65 - Version bump

Issue - State: closed - Opened by andreas-wilm over 4 years ago - 3 comments

#64 - Write to bam/cram instead of sam

Issue - State: closed - Opened by mflevine over 4 years ago - 3 comments

#63 - bai index

Issue - State: closed - Opened by gatozee over 4 years ago - 8 comments

#62 - hts-1.10 assertion failed

Issue - State: closed - Opened by slw287r over 4 years ago - 3 comments

#61 - Changed the iterator BGZI.query start/stop parameters to int64.

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

#60 - Multiple iterators with items*(v:VCF)

Issue - State: closed - Opened by cvlvxi over 4 years ago - 3 comments

#59 - VCF: Clear all INFO field

Issue - State: closed - Opened by cvlvxi over 4 years ago - 2 comments

#58 - Issue with vcf.nim when running nimble test or importing

Issue - State: closed - Opened by NatPRoach over 4 years ago - 3 comments

#57 - Vcf FORMAT missing values.

Issue - State: closed - Opened by cassimons almost 5 years ago - 7 comments

#56 - did recent change break nim CI ?

Issue - State: closed - Opened by timotheecour almost 5 years ago - 3 comments

#55 - How to build new variants?

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

#54 - FFI: Import C stdlib functions by header

Pull Request - State: closed - Opened by dbeinder almost 5 years ago - 1 comment

#53 - handle htslib 1.10

Issue - State: closed - Opened by brentp almost 5 years ago - 1 comment

#52 - Get query length from CIGAR?

Issue - State: closed - Opened by sdwfrost almost 5 years ago - 2 comments

#51 - fetch contigs and lengths

Issue - State: closed - Opened by danielecook about 5 years ago - 13 comments

#50 - Prepare for csize to be uint

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

#49 - static builder failed

Issue - State: closed - Opened by lch14forever about 5 years ago - 8 comments

#47 - Auto-test the Readme.md code.

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

#46 - Added ability to set ID in VCF Variants

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

#45 - Added ability to set ID in VCF Variants

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

#44 - Fix warnings

Pull Request - State: closed - Opened by pb-cdunn about 5 years ago - 4 comments

#43 - Request: addition to wiki/Examples

Issue - State: closed - Opened by andreas-wilm over 5 years ago - 4 comments

#42 - set tag/ append tag

Issue - State: closed - Opened by ruqianl over 5 years ago - 1 comment

#41 - modify qname

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

#40 - Explort ploidy field

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

#39 - expose hrec

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

#38 - error opening index

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

#37 - conditional iterator

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

#36 - Alpine

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

#35 - Add iterator to read BGZ files line by line

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

#34 - Iteration without for loop

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

#33 - proc to remove format/info field in header

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

#32 - vcfs from scratch

Pull Request - State: closed - Opened by mflevine over 5 years ago - 8 comments

#31 - HTS-lib dependency

Issue - State: closed - Opened by jaudoux almost 6 years ago - 15 comments

#30 - Write new VCF files

Issue - State: closed - Opened by mflevine almost 6 years ago - 7 comments

#29 - Undeclared routine: `aux`

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

#28 - Format strings

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

#27 - Q: best practices to read vcf from stdin or string

Issue - State: closed - Opened by andreas-wilm almost 6 years ago - 5 comments

#26 - Undocumented and possibly broken functions

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

#25 - Q: how to read BAM from internally generated stream

Issue - State: closed - Opened by andreas-wilm about 6 years ago - 5 comments

#24 - Fixing the BAM-SAM-CRAM example in README.md

Pull Request - State: closed - Opened by andreas-wilm about 6 years ago - 1 comment

#23 - Fixing the sample code.

Pull Request - State: closed - Opened by xbello about 6 years ago - 2 comments

#22 - add strings method for FORMAT type

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

#21 - expose more fai stuff? (and some slowness with Fai.get())

Issue - State: closed - Opened by kmhernan over 6 years ago - 4 comments

#20 - Tests crash

Issue - State: closed - Opened by pb-cdunn over 6 years ago - 14 comments

#19 - does not work with extra fields of type 'A'

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

#18 - fixes retrieval of char-type extra fields

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

#17 - Does this library work with SAM files?

Issue - State: closed - Opened by nellore over 6 years ago - 5 comments

#16 - Api

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

#15 - Consider adding additional getters in BAM

Issue - State: closed - Opened by nh13 over 6 years ago - 2 comments

#14 - qual is ambiguous, reconsider naming to mapq or mapping_quality

Issue - State: closed - Opened by nh13 over 6 years ago - 2 comments

#13 - Question: what is the SAM_RGAUX flag?

Issue - State: closed - Opened by nh13 over 6 years ago - 1 comment

#12 - Question: whats the "back" value represent in CigarOp?

Issue - State: closed - Opened by nh13 over 6 years ago - 2 comments

#11 - Names for Op and CigarOp are confusing at first glance

Issue - State: closed - Opened by nh13 over 6 years ago - 4 comments

#10 - Suggestion: Handling of SAM optional tags

Issue - State: closed - Opened by nh13 over 6 years ago - 3 comments

#9 - Expose an interface to populating strings in the INFO field

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

#8 - README examples should be tested

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

#7 - Make example code in the README compile

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

#6 - can't clone project properly

Issue - State: closed - Opened by unikzforce almost 7 years ago - 3 comments

#5 - how to install and use?

Issue - State: closed - Opened by unikzforce almost 7 years ago - 1 comment

#4 - libname typo for macosx

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

#3 - new module: fai allow random access to fasta files with an index

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

#2 - Csi

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

#1 - nim-ify code

Issue - State: closed - Opened by brentp about 7 years ago - 1 comment