Write `QNAME` of reads that failed QC to a separate file

[PeteHaitch]

Rather than just output these to STDOUT, create a file of the QNAME and the reason a read was filtered out during QC steps. Add the option to not create this file which instead would direct this output to /dev/null

[PeteHaitch]

Reasons that reads can fail QC:

• Missing or incompatible XR or XG-tag (this is checked multiple times, can probably remove some of these checks)
• Missing 0x01, 0x40 or 0x80 FLAG bit (paired-read FLAG information)
• XG or XR-tags for are inconsistent with OT-strand or OB-strand (checked multiple times)
• Invalid comethylation_state
• read_1 or read_2 does not appear to be correctly set (should only happen if for some reason one of the mates is missing or in the wrong position in the queryname sorted BAM
• mapQ < threshold
• Skipping single-end read as positions aren't properly ordered (Case A).
• Skipping readpair as overlapping sequence does not pass filter specified by --overlappingPairedEndFilter
• Skipping paired-end read as positions aren't properly ordered (Case 1).
• Skipping paired-end read as positions aren't properly ordered (Case 1: shared m-tuples).
• Skipping paired-end read as positions aren't properly ordered (Case 2).
• Skipping paired-end read as positions aren't properly ordered (Case 2: shared m-tuples).
• Skipping read-pair as it is not properly paired.
• Skipping readpair as reads aligned to different chromosomes

This will be simplified to the following categories:

• [x] WARNING Invalid comethylation_state
• [x] WARNING Paired end read missing its mate or its mate is out of place
• [x] WARNING Fails the --overlappingPairedEndFilter
• [x] WARNING Read contains indels
• [x] WARNING mapQ < threshold
• [x] WARNING Read-pair is not properly paired
• [x] WARNING Read or its mate is unmapped
• [x] WARNING Mates of read-pair are mapped to different chromosomes
• [x] WARNING Read is a duplicate
• [x] ERROR Reads are from the non-directional bisulfite-sequencing protocol
• [x] ERROR Can't tell if read is single-end or which mate of a paired-end read
• [x] ERROR Missing or incompatible XR or XG tag
• [x] ERROR The positions in the m-tuple aren't correctly sorted

[PeteHaitch]

Reads that fail QC will be written to the file <sampleName>.reads_that_failed_QC.txt along with a message describing why the read failed. It might be a good idea to gzip this file to save space.

Additionally, a tally of the number of reads that failed each QC step will be reported to STDOUT.