SeqLib

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Currently, BamRecord objects have a FirstRead() method that returns `true` if the 0x40 bit of the FLAG field is set. This PR proposes adding a corresponding LastRead() method that returns...

nathanweeks

Use system htslib; a couple minor tweaks

2

The htslib submodule was getting stale; I think it's better if we use whatever system htslib is already included. Also implemented a more efficient way of getting the number of...

julianhess

hi

1

lqsae

Hi, it seems that the function ProperOrientation returns the read pairs in FR. But in the code: if (b->core.pos < b->core.mpos) { return (b->core.flag&BAM_FREVERSE) == 0 && (b->core.flag&BAM_FMREVERSE) != 0...

linhxxx

Name space pollution - there is another seqlib

4

Hi, in the COVID-19 fighting effort of the Debian Med team where we try to package software that is relevant to do research on COVID-19 I stumbled upon seqlib as...

tillea

BamReader::SetCramReference

3

Hello, I'm unable to reliably read from a CRAM file when using `BamReader::SetCramReference()`. ``` Failed to populate reference for id 4 Unable to fetch reference #4 16121..256523 ``` Since I'm...

agraubert

Version 1.1.2 has changed API

1

Hi, in Debian we have invented an ABI version 0 to flag once a library has changed its interface. I realised that you have removed some symbols. For instance TrainAndCorrect...

tillea

Hi, The link to the C++ API documentation is broken, could you please fix it? https://walaj.github.io/seqlibdocs/doxygen Thanks!

rkostadi

Undefined Constructor for template class GenomicRegionCollection

1

Several constructor declared in GenomicRegionCollection.h are not defined in GenomicRegionCollection.cpp, resulted in failed compilication with undefined reference error code.

yonghanyu

I'm getting a heap overflow associated with memory set in the SetCigar function. The simplest way to reproduce the problem is: #include #include #include #include #include #include #include "SeqLib/RefGenome.h" #include...

Ahhgust