javier mapping issue (npev)

[aineniamh]

have now added in a file that gets greated for each barcode- it details why a given read is not included or is included in the mapped reads section. Reasons include:

• read too short
• read too long
• mapping quality too low
• aln block length too short
• ambiguous mapping (same read mapped to two different places)

[aineniamh]

suspect this is related to the issue caused by #188 sequences added where mapping quality is too low if conflicting sequences in db. EV mode could have a lower mapping quality threshold