Ecosyste.ms: Issues

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GitHub / lh3/bwa issues and pull requests

#336 - Add the header line to the output SAM

Pull Request - State: closed - Opened by nh13 almost 3 years ago - 1 comment

#335 - bwa mem not set proper pair flag

Issue - State: open - Opened by Frank1219 about 3 years ago - 2 comments

#334 - Reads aligning to hard masked regions with Ns

Issue - State: open - Opened by hp2048 about 3 years ago

#332 - Moved source files to src

Pull Request - State: closed - Opened by Stefan-Schroder about 3 years ago

#330 - Add the mate mapping quality tag

Pull Request - State: closed - Opened by nh13 over 3 years ago - 1 comment

#329 - PACBIO contigs with BWA-MEM

Issue - State: closed - Opened by khush876 over 3 years ago - 2 comments

#328 - bwa_mem

Issue - State: open - Opened by 123123456abc over 3 years ago

#327 - Resume

Issue - State: open - Opened by ardy20 over 3 years ago

#326 - flag settings for perfect-matched alignments

Issue - State: open - Opened by zhenzhenyang-psu over 3 years ago

#323 - Wrong SAM file header generated with BWA -mem option

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

#318 - Fail to index human genome in a shell with 120Gb memory

Issue - State: open - Opened by yangyxt over 3 years ago - 2 comments

#316 - Cpp compatability

Pull Request - State: closed - Opened by starling13 almost 4 years ago

#314 - BWA compile fail with GCC 10

Issue - State: open - Opened by fizwit almost 4 years ago - 6 comments

#313 - bwa index problem when indexing files with large size

Issue - State: open - Opened by 544728460 almost 4 years ago - 8 comments

#309 - Convert "properly read" constants to command line parameters

Pull Request - State: open - Opened by gdgib-roche almost 4 years ago - 1 comment

#307 - Installation: No rule ... stop messages

Issue - State: open - Opened by mdhar1980 almost 4 years ago - 2 comments

#301 - Log verbosity

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

#300 - Does not compile for ARM

Issue - State: open - Opened by mattchatporter about 4 years ago - 14 comments

#298 - the flag of bam

Issue - State: open - Opened by tyyiyi about 4 years ago - 1 comment

#297 - Clarify bwa mem -5 option

Pull Request - State: closed - Opened by nh13 over 4 years ago

#294 - allow the user to specify the XA drop ratio via the -z option

Pull Request - State: closed - Opened by nh13 over 4 years ago

#293 - Output mapping quality with XB

Pull Request - State: closed - Opened by nh13 over 4 years ago

#292 - Document "-u"

Pull Request - State: closed - Opened by nh13 over 4 years ago - 2 comments

#290 - paired end read name problems

Issue - State: open - Opened by dpellow over 4 years ago - 1 comment

#289 - BWAKit run-gen-ref can't get files for resource-GRCh38

Issue - State: open - Opened by jtm732 over 4 years ago - 1 comment

#283 - travis: added arm64, ppc64le and s390x tests with simde

Pull Request - State: open - Opened by junaruga over 4 years ago - 6 comments

#276 - bwa mem "killed" in docker container

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

#275 - make is failed on gcc 10

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

#263 - Makefile: Use $CPPFLAGS and $LDFLAGS if they are set

Pull Request - State: closed - Opened by jmarshall almost 5 years ago - 2 comments

#256 - BWA-MEM doesn't return all matches (very short sequences)

Issue - State: closed - Opened by Permafacture about 5 years ago - 7 comments

#251 - Maximum number of bases for a reference genome

Issue - State: open - Opened by xie186 about 5 years ago - 3 comments

#231 - How to create .alt index file?

Issue - State: closed - Opened by hp2048 almost 6 years ago - 10 comments

#228 - Paired reads have different names

Issue - State: open - Opened by MichaelVirology almost 6 years ago - 13 comments

#222 - Incorrect report of mapped reference name for short reads.

Issue - State: open - Opened by kingdynasty about 6 years ago - 2 comments

#211 - NH tag

Issue - State: open - Opened by apredeus over 6 years ago - 4 comments

#202 - Implement -v/--version option

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

#184 - [W::sam_read1] parse error at line 1

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

#165 - Mate rescue shifts alignment at "unseen" indel

Issue - State: closed - Opened by hzpc-joostk about 7 years ago

#158 - bwa mem: Passing a variable to read group

Issue - State: closed - Opened by royfrancis about 7 years ago - 3 comments

#146 - Memory overrun issue in bwasw (via valgrind)

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

#137 - TLEN reported by BWA MEM for some templates seems to be wrong

Issue - State: open - Opened by soumitrakp over 7 years ago - 3 comments

#120 - Assertion in bntseq fails

Issue - State: open - Opened by ahwagner over 7 years ago - 12 comments

#113 - explanation of insert sizes from BWA-MEM

Issue - State: open - Opened by roblanf over 7 years ago - 18 comments

#104 - Multithread support for bwa index

Issue - State: closed - Opened by unode almost 8 years ago - 13 comments

#99 - Output for unmapped pair

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

#77 - Fails compile on POWER8: SSE2 intrinsics -> VSX/AltiVec

Issue - State: closed - Opened by jlost over 8 years ago - 3 comments

#75 - bwa index problem

Issue - State: open - Opened by gsong1205 over 8 years ago - 1 comment

#24 - Multi comma-separated fastq for bwa-mem.

Pull Request - State: open - Opened by lindenb over 10 years ago - 1 comment