Merge pull request #63 from wtsi-npg/devel

1.12 release
Merge pull request #66 from wtsi-npg/devel

Release 1.13
Merge pull request #67 from jenniferliddle/devel

Handle secondary alignments
Merge pull request #1 from wtsi-npg/devel

get updates from wtsi devel
Fix typo in method name: readRunfoder
reduced HiSeqX runfolder for testing
ensure the readname does not start with :, Illumina X10 instruments: one loc file for all lanes and tiles
allow for absence of run id and instrument info in the configuration file
Merge branch 'devel' into HEAD
whitespace
HiSeqX runfolder has no config xml files

so try to pick missing informationf fomr runParamters and RunInfo
xml files
HiSeqX runfolder has no config xml files

so try to pick missing information from runParameters and RunInfo
xml files
Enable Travis-CI
Update versions (to 1.15) ready for release
Merge pull request #69 from dkj/devel

Cope with HiSeqX runfolders
Merge pull request #70 from wtsi-npg/devel

pull request from wtsi devel to master to create release 1.15
to pass tests after the version update, up the harcoded programVersion field in test data; add TODO note
Merge pull request #71 from wtsi-npg/master

pull changes from wtsi master (version 1.15) to devel
bugfix: index reads should not be merged if second BC paramters given
Add test data and inital test for dual index run