misleading graphics output when running a concatenated reference file

[figueroakl]

sent the directory I tested this on to gitter

MapvsUnmap reads does not seem to map the mapped reads percentage for some samples when running against a concatenated reference file? Could it be a sequential issue, such as, the reads got to the first reference in the file and that leads to the other references to be ignored?

[averagehat]

[averagehat]

[averagehat]

Den4_CummingsRefsConcat.txt
flagstats.txt

[averagehat]

13784.bam.consensus.fasta.txt
13784.bam.qualdepth.json.txt

[averagehat]

Looks like a bug in samtools.MPileupColumn(line)

used here

ngs_mapper/ngs_mapper/bqd.py

Line 46 in 92f8665

mcol = samtools.MPileupColumn(line)

<-- this is where qualdepth.json gets messed up
and here https://github.com/VDBWRAIR/ngs_mapper/blob/master/ngs_mapper/base_caller.py#L384 <-- where consensus/vcf get messed up

[averagehat]

ngs_mapper/ngs_mapper/bam_to_qualdepth.py

Line 17 in 92f8665

pileup = bqd.parse_pileup( pileup )

[averagehat]

samtools mpileup is only returning 67 rows, all with depth=1

[averagehat]

The problem seems to be that almost all mappings are "anomalous read pairs" or "orphans"
I'm not clear why that's happening with these samples, and with multi-entry reference fastas.
This isn't a bug, as far as I can tell.
see #112 #8

[figueroakl]

I'm going to look over the issues you and try to make sense of it.

[averagehat]

Determined the reads are orphans; a little more info is in gitter. The solution is to make allowing orphans (-A in samtools) a configurable option

[averagehat]

Have to rework some functions, update where they are called, and pass the config around more...

base_caller: samtools.mpileup
graphsample: samtools.nogap_mpileup
bam_to_qualdepth: samtools.nogap_mpileup; bam.get_refstats; bam.alignment_info;
tagreads: samtools.view (x2)-- can just add A=True
stats_at_refpos: samtools.mpileup
bqd is clear of system calls

tagreads - gets config, sort of
base_caller gets config
graphsample does not get config (?)

flagstats?