Version 1.2.0

The following bugs have been fixed in the update from version 1.1.6 to v1.2.0:+

Major:

• In version 1.1.6 after running the StartWithBam function analyzing a region having a coverage of 0, the normalized coverage would have a value of -NaN. This issue is fixed in version 1.2.0, by adding the -a flag to the samtools depth function. However, this causes a dependency on samtools version 1.3 or higher.
  In version 1.1.6 HOM_DEL and HOM_DUP calls were interpreted as separate events as DEL and DUP calls.
• This could cause calls to be cut into several pieces and create gaps in the calls because of downstream filtering. Now, HOM_DEL calls are interpreted as part of a DEL call as well as a separate call. For instance if exons 1 and 3 have a DEL call in the totallist and exon 2 a HOM_DEL call. A deletion of exons 1 to 3 will be called as well as a homozygous deletion of exon 2. Similarly HOM_DUP events are considered as part of DUP events as well as a separate call. Note that in case all targets of a call are considered HOM_DEL or HOM_DUP the call will appear twice on the longlist, shortlist and/or finallist.

Minor:

• In the StartWithMatchScore function the 'Avg abs diff incl sex' was showing the same value as the 'Avg abs diff autosomal'. Now the values are correct.
• A bedfile containing UCSC style notation 'chr1, chr2, etc.' is now be compatible with a header notation of '1, 2, etc.'
• The finallist is now called finallist.txt instead of shortlist.finallist.txt.
• In the log file produced during the StartWithBestScore function SAMPLE_RATIO has been renamed SAMPLE_CV.
• The inputDir is not a requirement anymore for the GenerateTargetQCList function.
• In the GenerateTargetQC function the searchpattern is changed to prevent the step trying to process files other than normalized coverage files.
• The used commandline options and values are now printed to the stdout by default.