Support of uBAM file

[ikit]

:+1:

[natir]

@ikit Where I can find the uBAM specification format ?

[natir]

Wheel,

We can use bamtools to read sam, bam and unaligned bam file.

But add this dependency maybe become hard (multi-plateform trouble), I work on this.

[natir]

Ok with htslib we can read uBAM file actualy we can detect the BAM file format and open the file. But when I try run analysis, FastQt generate a segfault, I don't know if is my file or is the code. @dridk you know where I can get a standard bamfile ?

[dridk]

You can find fastq, bam and vcf file here : http://www.internationalgenome.org/data-portal/sample Why not using htslib to read bam ? You can check the code from https://github.com/labsquare/CuteVCF

[natir]

@dridk we use htslib to read bam

[dridk]

Sorry, I was reading the old mesage with bamtools

[natir]

Well,

I think the support of ubam file is ready, I use the quality mapping field for sequence quality.

For test, I convert a fastqt file with this gatk tutoriel, the result is similar when we use fastqt or ubam.

I want reread code for remove deadcode, no C++ code, and search some bug, but this issue is close to be closed :)

[natir]

Ok htslib branch is ready to merge, maybe we need check this branch run on windows before, merging in devel.

We can't have a progression bar for ubam/bam file.

[natir]

@dridk @ikit or other people can check if htslib branch is fully functional and code isn't too ugly.

[dridk]

I get unexpected crash with all bam tested :

[dridk]

Don't understand... aln->core.l_qseq return always 0. I tested other parameter like chromosom and position. They works