[Debian-med-packaging] Bug#753485: Bug#753485: Status of samtools

[Charles Plessy]

Le Thu, Sep 18, 2014 at 09:22:45AM +0200, Andreas Tille a écrit :
> On Thu, Sep 18, 2014 at 07:42:52AM +0900, Charles Plessy wrote:
> > 
> > I have not uploaded yet samtools 1.0 to Unstable, because it strangely fails to
> > build in a chroot, where two regression tests do not pass.
> > 
> > When comparing the logs of the building with git-buildpackage (local, works)
> > and sbuild (chroot, fails), the only significant difference that I see is for
> > the failure itself:
 
> Is this for the current state of Git?  I tried with this and got in a pbuilder
> environment:

Hi Andreas,

in summary, build works from Git, from pbuilder, but not from sbuild (I just tried
on another machine).  The problem is that our autobuilders use sbuild…

What could be the cause of the failure ?  I still do not understand.  In my
latest tests, it appears that when building in a sbuild chroot, the command
'samtools stats' returns an empty result instead of the usual help message,
which causes the regression test for help messages to fail.  However, the
binary package produced when disabling the test suite runs the command
normally.

Expected output:

	About: The program collects statistics from BAM files. The output can be visualized using plot-bamstats.
	Usage: samtools stats [OPTIONS] file.bam
	       samtools stats [OPTIONS] file.bam chr:from-to
	Options:
	    -c, --coverage <int>,<int>,<int>    Coverage distribution min,max,step [1,1000,1]
	    -d, --remove-dups                   Exclude from statistics reads marked as duplicates
	    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]
	    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]
		--GC-depth <float>              the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
	    -h, --help                          This help message
	    -i, --insert-size <int>             Maximum insert size [8000]
	    -I, --id <string>                   Include only listed read group or sample name
	    -l, --read-length <int>             Include in the statistics only reads with the given read length []
	    -m, --most-inserts <float>          Report only the main part of inserts [0.99]
	    -q, --trim-quality <int>            The BWA trimming parameter [0]
	    -r, --ref-seq <file>                Reference sequence (required for GC-depth and mismatches-per-cycle calculation).
	    -t, --target-regions <file>         Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.
	    -s, --sam                           Input is SAM (usually auto-detected now).
	    -x, --sparse                        Suppress outputting IS rows where there are no insertions.


Extract from the output seen by the test suite when run with sbuild (collected
by inserting “say `samtools stats`” in the test suite.

	# This file was produced by samtools stats (1.0+htslib-1.0) and can be plotted using plot-bamstats
	# The command line was:  stats
	# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
	SN	raw total sequences:	0
	SN	filtered sequences:	0
	SN	sequences:	0
	SN	is sorted:	1
	SN	1st fragments:	0
	SN	last fragments:	0
	SN	reads mapped:	0
	SN	reads mapped and paired:	0	# paired-end technology bit set + both mates mapped
	SN	reads unmapped:	0
	SN	reads properly paired:	0	# proper-pair bit set
	SN	reads paired:	0	# paired-end technology bit set
	SN	reads duplicated:	0	# PCR or optical duplicate bit set
	SN	reads MQ0:	0	# mapped and MQ=0
	SN	reads QC failed:	0
	SN	non-primary alignments:	0
	SN	total length:	0	# ignores clipping
	SN	bases mapped:	0	# ignores clipping
	SN	bases mapped (cigar):	0	# more accurate
	SN	bases trimmed:	0
	SN	bases duplicated:	0
	SN	mismatches:	0	# from NM fields
	SN	error rate:	0.000000e+00	# mismatches / bases mapped (cigar)
	SN	average length:	0
	SN	maximum length:	30
	SN	average quality:	0.0
	SN	insert size average:	0.0
	SN	insert size standard deviation:	0.0
	SN	inward oriented pairs:	0
	SN	outward oriented pairs:	0
	SN	pairs with other orientation:	0
	SN	pairs on different chromosomes:	0
	# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.
	# Columns correspond to qualities and rows to cycles. First column is the cycle number.
	FFQ	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0
	FFQ	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0
	FFQ	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0
	FFQ	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0
	FFQ	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0
	FFQ	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00	0	0	0	0	0	0	0	0	0
	FFQ	7	0	0	0	0	0	0	0	0	

This is the kind of output that one would see when running samtools stats on
actual data, for example test/stat/1_map_cigar.sam, except that with actual
data the numbers will not all be zero.

If somebody has a good idea…

Have a nice day,

-- 
Charles