Dash in SAM
Output folder path issue
Merge pull request #1 from night-stalker/master

SAM file bugs
Latest version, bugfixes.
Wobbles are allowed in reference genome
consensus needs to be fixed.
Reports NM:i AS:i and RC as flag
Report gap open and extend costs as X? and Y?, respectively.
FLAGS are set properly. Report gap open and extend costs as XE and XO, respectively.
Reverse flag set properly for single-end reads
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Consensus with wobbles, refines works again, consensus is full-length, -mcc
Readme
v1.0
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