LongReads: remove unmapped bams

[leonschuetz]

• fix bug in mapping pipeline:

  • reads are lost during mapping
  • determine step and fix

• add check for sufficient file size/read count in mapped BAM

• remove unmapped BAM according to project setting

• add CRAM support:

  • check if cram can be used for downsteam analysis
  • if not: implement code to unpack it on-the-fly

[leonschuetz]

• integrate new longphase version
  • should be fixed in 1.7.2

[leonschuetz]

• cram corrupted after Calling -> longphase?

[leonschuetz]

• samtools reports 0 reads for whole chrs, but section contain reads
• also some times after mapping
• can be solved by resorting the file (not only re-writing)
• test mapping seperately

[leonschuetz]

• test special CRAM options for methylation

[leonschuetz]

• tests on HG001/HG002: 0/5 reads missing
  • all reads are duplicates in original bam file (re-base called?)
• test on set of diagnostic samples
• add function to check BAMs (chr-wise)
• add checks at each point on which the BAM/CRAM is modified