Andrew Whitwham issues

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                                            Andrew Whitwham

Changed the default UMI barcode regex.

The default UMI barcode regex was too restrictive. This change broadens the pattern it will accept. The example given in Illumina's documentation should now be accepted. e.g. NDX550136:7:H2MTNBDXX:1:13302:3141:10799:AAGGATG+TCGGAGA Fixes #1730.

Fix hard clip quality left hand side score.

When hard clipping the left hand side of an alignment the quality score was being trimmed from the right hand side. The will quality score will now be trimmed from...

fixmate no longer removes PAIRED flag.

No longer removes paired flag from reads that have no mate (either removed or missing). Fixes #2052 using the idea that the PAIRED flag is a sequencing technology indicator not...