Filter out bwa mem PE poor alignments

[colindaven]

Related to the problems with softclipping - #88

There is a new (since samtools 1.12 ) set of filter expressions in samtools.

http://www.htslib.org/doc/samtools.html#FILTER_EXPRESSIONS

• samtools upgrade in conda env needed - created
• add env via new branch and PR to wochenende
• implement filter methods, possibly combine others to increase performance ?
• test
• check of rlen >150 would work for PE reads, ie is the ref length per read or per read pair?

rlen | int | Alignment length: no. reference bases

If we use say rlen 70+ for PE reads we can force good alignments without modifying the score too much.

eg

samtools view -e 'rlen>70' -O BAM -o out.bam in.bam