Ecosyste.ms: Issues

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

GitHub / lh3/bwa issues and pull requests

#436 - bwa index of 300GB multifasta fails at bwt2sa stage without error

Issue - State: closed - Opened by hazmup about 1 month ago - 3 comments

#434 - After running make，I did not see ref.fa

Issue - State: open - Opened by tudousiZzz 2 months ago

#433 - Sequence mapping only when complement

Issue - State: closed - Opened by 7PintsOfCherryGarcia 2 months ago

#430 - Cannot allocate memory

Issue - State: open - Opened by emilyhokning 3 months ago

#427 - How can i obtain all the regions reads hit. (in duplication region)

Issue - State: closed - Opened by liukeweiaway 4 months ago - 2 comments

#426 - fixed a compiler error

Pull Request - State: open - Opened by kemin711 4 months ago

#425 - Continuation after error "paired reads have different names"

Issue - State: open - Opened by scg40 4 months ago - 1 comment

#424 - BWA and short read mapping

Issue - State: open - Opened by alessandromacc 5 months ago

#423 - the significance of the -V parameter and XR tag

Issue - State: open - Opened by YettaWang 5 months ago

#422 - How are ambiguity charaters handled in BWA?

Issue - State: open - Opened by SaitouAsuka 5 months ago

#418 - Is there MD tag in output of bwa?

Issue - State: open - Opened by YuanHank 7 months ago

#417 - missing `bwa-0.7.18.tar.bz2` for 0.7.18 release

Issue - State: open - Opened by chenrui333 7 months ago - 1 comment

#415 - no ID within the read group line

Issue - State: open - Opened by FengjuanjuanCMS 8 months ago

#414 - Fix `kt_for()` declaration parameter types

Pull Request - State: open - Opened by jmarshall 8 months ago

#413 - Indexing large genome failed

Issue - State: open - Opened by xzhoubayer 8 months ago - 3 comments

#412 - [M::bwa_idx_load_from_disk] read 0 ALT contigs

Issue - State: open - Opened by erah1 8 months ago

#411 - Build fails with LTO

Issue - State: open - Opened by eli-schwartz 9 months ago

#409 - Fail to read header from fasta input

Issue - State: open - Opened by gustavogregoracci 12 months ago

#408 - Did bwa index use the SA-IS algorithm?

Issue - State: open - Opened by MiyaaL 12 months ago

#407 - bwa mem hangs after a few thousand reads

Issue - State: open - Opened by chklee30 12 months ago

#406 - how to eliminate the effects of estimated insertion size distribution

Issue - State: closed - Opened by Ben-unbelieveable about 1 year ago - 1 comment

#404 - Question about XA Tag and MAPQ Values

Issue - State: closed - Opened by zqlns about 1 year ago - 1 comment

#402 - Non-text characters appearing in SEQ field

Issue - State: open - Opened by csoeder about 1 year ago

#401 - Time to release new version?

Issue - State: closed - Opened by Yikun about 1 year ago - 8 comments

#399 - The bwa index is faulty

Issue - State: closed - Opened by heweihuang over 1 year ago

#397 - [mem] reads are not labelled as proper pair

Issue - State: open - Opened by ftian9 over 1 year ago

#396 - clipping penalty

Issue - State: open - Opened by FarGlasgow over 1 year ago

#395 - bwa mem different result in repetitive test

Issue - State: closed - Opened by baoyl818 over 1 year ago - 1 comment

#393 - BWA BAM

Issue - State: open - Opened by duhuipeng over 1 year ago - 3 comments

#392 - Left-most alignment of gaps?

Issue - State: closed - Opened by eranbio over 1 year ago - 1 comment

#391 - Fix RNEXT output in xa2multi.pl

Pull Request - State: open - Opened by tsnorri over 1 year ago

#390 - xa2multi.pl outputs RNEXT w.r.t. original alignment

Issue - State: open - Opened by tsnorri over 1 year ago - 1 comment

#389 - Can I use Apache2 branch under Apache 2.0 license?

Issue - State: open - Opened by pasang0000 over 1 year ago

#388 - question on mapping to short reference like 1kb

Issue - State: open - Opened by jianshu93 almost 2 years ago

#387 - Error coming during compilation

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

#386 - bwa mem failed to locate index files

Issue - State: open - Opened by isabelluo almost 2 years ago - 1 comment

#385 - Update rle.h

Pull Request - State: closed - Opened by hartleys almost 2 years ago

#383 - run-gen-ref

Issue - State: open - Opened by StefanoLise almost 2 years ago

#382 - bwa mem -a and -t options are incompatible?

Issue - State: open - Opened by yazhinia almost 2 years ago

#381 - mapping on subset of a bigger reference gives different results

Issue - State: open - Opened by mewu3 almost 2 years ago

#380 - A error ouput for bwa mem

Issue - State: open - Opened by fengchuiguo1994 almost 2 years ago

#379 - Multimapping and reference sequence junctions

Issue - State: open - Opened by s-a-nersisyan about 2 years ago

#377 - bwa mem -a output all alignments for SE or unpaired PE

Issue - State: open - Opened by fanshu1986 about 2 years ago - 1 comment

#376 - bwa mem or bwa sw

Issue - State: open - Opened by Oksanak22 about 2 years ago

#375 - bwa mem ont2d

Issue - State: closed - Opened by Oksanak22 about 2 years ago - 2 comments

#374 - re compiling bwa on mac (M1)

Issue - State: open - Opened by haircell about 2 years ago - 2 comments

#372 - Number of characters per line for a reference sequence

Issue - State: open - Opened by olu2016 about 2 years ago

#371 - Trailing whitespace in SAM file

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

#370 - tied matches of bwa and bowtie2

Issue - State: closed - Opened by jianshu93 over 2 years ago - 1 comment

#369 - Added -fPIC as compile flag

Pull Request - State: open - Opened by lennykovac over 2 years ago

#368 - Add HLA-DPB1 typing

Issue - State: open - Opened by Gerde over 2 years ago

#367 - Add CI job for Ubuntu 20.04 aarch64

Pull Request - State: closed - Opened by martin-g over 2 years ago - 3 comments

#366 - add break condition to making cigar string

Issue - State: open - Opened by gayoung93 over 2 years ago

#365 - add condition to BSW in case of reversing

Issue - State: open - Opened by gayoung93 over 2 years ago

#364 - Adding chm13 option in bwakit

Issue - State: open - Opened by mikecuoco over 2 years ago

#363 - T2T-CHM13 index file not recognized

Issue - State: open - Opened by abbeythorpe over 2 years ago

#362 - add break condition to making cigar string

Pull Request - State: open - Opened by gayoung93 over 2 years ago

#361 - add condition to BSW in case of reversing

Pull Request - State: open - Opened by gayoung93 over 2 years ago

#360 - Different alignment numbers to same reference sequence

Issue - State: open - Opened by stewalsh04 over 2 years ago

#359 - Add ARM Neon and scalar implementations of SIMD functions

Pull Request - State: closed - Opened by jmarshall over 2 years ago - 8 comments

#358 - bwa aln returning less alignments for higher number of mismatches

Issue - State: open - Opened by Jfortin1 over 2 years ago - 2 comments

#357 - bwa mem fails to identify paired-end sequences with 'not enough pairs' message

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

#356 - Bug: bwa aln misreports alignment contigs

Issue - State: open - Opened by mattsoup over 2 years ago - 1 comment

#355 - Document that the XB tag now contains the mapping quality too

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

#354 - the 1st file has fewer sequences

Issue - State: open - Opened by happyrainbows over 2 years ago

#353 - install bwa 0.7.17 in alpine docker image

Issue - State: open - Opened by cmccabe0728 over 2 years ago - 1 comment

#352 - how to attach XM tag

Issue - State: closed - Opened by S-111 over 2 years ago - 1 comment

#349 - Failed Installation on MacOS M1

Issue - State: open - Opened by josoga2 over 2 years ago - 1 comment

#348 - Use SAM headers from index directory's `<prefix>.hdr` if it exists

Pull Request - State: open - Opened by jmarshall over 2 years ago - 6 comments

#346 - Avoid conflicting with HTSlib's kstring.c functions

Pull Request - State: open - Opened by jmarshall over 2 years ago

#345 - bugfix: HD line should be printed before SQ

Pull Request - State: closed - Opened by nh13 over 2 years ago - 2 comments

#344 - Add support for Arm/Aaarch64.

Pull Request - State: closed - Opened by nh13 over 2 years ago - 3 comments

#343 - Update bwa.1 to remove ancient reference to picard

Pull Request - State: closed - Opened by nh13 almost 3 years ago

#342 - postalt.js MAPQ 0 on both chr17 and Alternate Contigs

Issue - State: open - Opened by DarioS almost 3 years ago - 1 comment

#341 - Does increasing memory cause a difference in BWA results?

Issue - State: open - Opened by losted-star almost 3 years ago - 1 comment

#340 - Question about mate rescue and MAPQ. The same alignments, different results

Issue - State: closed - Opened by shenghuanjie almost 3 years ago - 1 comment

#339 - BWA aln runs slower for first time and subsequent runs are faster

Issue - State: open - Opened by rjg2186 almost 3 years ago - 4 comments

#338 - bwa mem - fastq sequence order

Issue - State: closed - Opened by Fazulur almost 3 years ago - 2 comments

#337 - genome .alt file

Issue - State: open - Opened by denise0593 almost 3 years ago