[Debian-med-packaging] Bug#736565: FTBFS on non-"PC" architectures: FAIL: scram_mt.test

[Charles Plessy]

Le Sun, Mar 09, 2014 at 10:10:28AM +0000, Aníbal Monsalve Salazar a écrit :
> 
> The regression test fails because xx#minimal.full.sam has one extra line
> at the end when it's compared to xx#minimal.full.bam.sam.
> 
> The extra line is:
> 
> A4	16	yy	4	1	*	*	0	0	*	*

Hi Aníbal,

The BAM format is the binary representation of the SAM format, for alignment of
nucleotide sequences on a reference genome.  I guess that the test suite checks
that the tool's output is the same in both formats, by converting BAM to SAM
and comparing the two SAM files.  Debian also distributes the 'samtools'
program, that can do this conversion as well.

$ samtools view -h xx#minimal.full.bam
@PG	ID:scramble	PN:scramble	VN:1.13.3	CL:/tmp/staden-io-lib-1.13.3/progs/.libs/lt-scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam 
@PG	ID:scramble.1	PN:scramble	PP:scramble	VN:1.13.3	CL:/tmp/staden-io-lib-1.13.3/progs/.libs/lt-scramble -t4 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram 
@PG	ID:scramble.2	PN:scramble	PP:scramble.1	VN:1.13.3	CL:/tmp/staden-io-lib-1.13.3/progs/.libs/lt-scramble -t4 -O bam test.out/xx#minimal.full.cram 
@SQ	SN:xx	LN:20	M5:bbf4de6d8497a119dda6e074521643dc	UR:/tmp/staden-io-lib-1.13.3/tests/./data/xx.fa
@SQ	SN:yy	LN:20	M5:bbf4de6d8497a119dda6e074521643dc	UR:/tmp/staden-io-lib-1.13.3/tests/./data/xx.fa
a0	16	xx	4	1	10H	*	0	0	*	*
a1	16	xx	4	1	10H	*	0	0	*	*
a2	16	xx	4	1	5H10M5H	*	0	0	AAAAAAATTT	*
A0	16	yy	4	1	*	*	0	0	*	*
A1	16	yy	4	1	*	*	0	0	*	*
A2	16	yy	4	1	*	*	0	0	*	*
A3	16	yy	4	1	*	*	0	0	*	*
A4	16	yy	4	1	*	*	0	0	*	*

Missing a line on MIPS definitely looks like a bug.  This said, it works on
amd64 (at least the test suite) and I doubt that there are users for the
staden-io-lib on MIPS.  Have you tried to contact the upstream author ?

Speaking of Upstream, I see a new release, version 1.13.5.  Would you like me
to upload it ?

Cheers,

Charles

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan