• Simpler input sorted check

• Introduced a sortedness check

• Fixed #12 When splitting the output by strand, if the coverage was not changing this resulted in inconsistent results.
• Added a check #13

When invoked without arguments, covtobed will print a message to inform the user that it is waiting for input from STDIN.

To suppress this message, set the environment variable COVTOBED_QUIET to 1.

Will warn to use samtools fixmate when physical coverage calculations result in unexpected coverage after the end of a contig. (#11)

This release introduces the -d flag to skip poor quality alignments that are:

• With mapping quality of 0 (a more stringent filter can be set)
• Duplicate alignments
• Non-primary alignments
• Failing vendor QC

Minor updates:

• When parsing an unsorted BAM it will raise an appropriate error
• Expanded test suite
• Expanded documentation

• This release supports coverage > 65,536 [#7]