walaj SeqLib issues - Githubissues

walaj / SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

http://bioinformatics.oxfordjournals.org/content/early/2016/12/21/bioinformatics.btw741.full.pdf+html

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issues

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Update submodules to work with GCC 10

#67 julianhess opened 1 year ago
4
BWA/Fermi submodules need update for GCC 10

#66 julianhess opened 1 year ago
0
Add LastFlag() to BamRecord

#65 nathanweeks closed 1 year ago
0
Use system htslib; a couple minor tweaks

#64 julianhess opened 3 years ago
2
Use system htslib, a couple minor tweaks

#63 julianhess closed 3 years ago
0
hi

#62 lqsae closed 1 year ago
2
function ProperOrientation() have a bug?

#61 linhxxx opened 3 years ago
0
upgrade to jsoncpp 1.9.4

#60 mr-c closed 3 years ago
1
`FermiAssembler` should take `fml_opt_t` assembly parameters from the user.

#59 cgroza closed 3 years ago
1
Build failure with newer libjsoncpp

#58 LocutusOfBorg closed 3 years ago
4
Added GFA output method call to FermiAssembler

#57 cgroza closed 4 years ago
0
Name space pollution - there is another seqlib

#56 tillea opened 4 years ago
4
The link to the doxygen API is broken

#55 rkostadi opened 4 years ago
0
Undefined Constructor for template class GenomicRegionCollection

#54 yonghanyu opened 4 years ago
1
Avoid using private HTSlib headers and functions

#53 jmarshall closed 3 years ago
5
heap-buffer-overflow

#52 Ahhgust opened 5 years ago
0
Try to infer b37 style contig names when constructing GenomicRegion from strings

#51 julianhess closed 4 years ago
0
Try to infer b37 style contig names when constructing GenomicRegion from strings

#50 julianhess closed 5 years ago
1
BamRecord's PositionEnd() inconsistent with Position()

#49 Ahhgust opened 5 years ago
0
determine if a quality string is empty

#48 ekg opened 5 years ago
0
Looking for functionalities to replace BamTools with SeqLib

#47 PauchardL opened 5 years ago
0
AlignmentPosition() is wrong with hard clips

#46 Ahhgust closed 5 years ago
3
Libraries are placed in {prefix}/bin and not {prefix}/lib

#45 edawson closed 5 years ago
1
Update makefile.am to build libs in lib/ rather than bin/

#44 edawson closed 5 years ago
1
kseq.h discarded the unaligned sequence name marker @, so we should a…

#43 wulj2 closed 5 years ago
0
Merge Request for some functionality enhancement

#42 wulj2 closed 5 years ago
3
Some functionality enchancement

#41 wulj2 closed 5 years ago
3
Should I update the htslib bwa to the latest version directly or need some code refactor?

#40 wulj2 closed 5 years ago
1
strongly advice to add SupplementaryFlag() in BamRecord.h

#39 wulj2 closed 5 years ago
0
Apply m_cram_reference to bams

#38 agraubert closed 5 years ago
1
Default Constructor may be optimized in case segment fault happens

#37 wulj2 closed 5 years ago
1
minor bug found

#36 wulj2 closed 5 years ago
1
ChrName function in BamRecord Class logic wrong

#35 wulj2 closed 5 years ago
1
BamReader::SetCramReference

#34 agraubert opened 5 years ago
3
SeqLib::BamWriter.WriteRecord() seems to be truncating the qname field

#33 bkohrn opened 5 years ago
2
Segmentation Fault when running

#32 bkohrn closed 5 years ago
3
Move BamReader forward declaration into SeqLib namespace

#31 dnbaker closed 6 years ago
1
Added functions to retrieve position of read accounting for soft clips

#30 julianhess closed 6 years ago
1
malloc(): smallbin double linked list corrupted

#29 rwdavies closed 6 years ago
1
fatal: unable to access 'https://github.com/walaj/SeqLib.git/': Peer's Certificate has expired.

#28 ShannonDaddy closed 6 years ago
3
fatal: unable to access 'https://github.com/walaj/SeqLib.git/': Peer's Certificate has expired.

#27 ShannonDaddy closed 6 years ago
0
Add different modes to BamWriter.Open

#26 1dayac opened 6 years ago
2
lzma.h: No such file or directory - but works for htslib 1.9

#25 jelber2 closed 6 years ago
2
Version 1.1.2 has changed API

#24 tillea opened 6 years ago
1
Close CRAM reference

#23 rwdavies opened 6 years ago
7
Example showing how to compile my own program containing SeqLib

#22 alifare closed 5 years ago
2
Could SeqLib and htslib work out what a public cram api should be?

#21 detrout closed 3 years ago
2
undefined reference to xx error for a test

#20 taojinsheng closed 5 years ago
8
incomplete error handling

#19 brentp opened 7 years ago
5
Paired end/mate mair reads

#18 Ahhgust opened 7 years ago
4