Version 1.5

Initial wiggle data are now rounded to three decimal places. This should reduce file size when run in -m (reads per million) mode.

Version 1.4

Added capability to generate a wig / bigwig file reporting on the fractions of reads within a specified size range. Newly added switch -i enables this mode.

Version 1.3

Add option -F, which is passed to samtools view -F to restrict using certain types of alignments in creating the coverage file(s).

The default option -F setting is 3844, which contains bits:
4 : unmapped reads
256: secondary alignments
512: Failed QC alignments
1024: PCR or optical duplicate alignments
2048: Supplementary alignments.

With the default setting of 3844, all of the above alignment types are ignored.
See SAM format specifications for more on the bitwise flags.

Version 1.2

Modified option -t to allow it to play nice with option -m. option -t now defaults to 0 instead of 1, and now is allowed to be a floating point number instead of just an integer. This allows fractional depths less than 1 (but above 0) to be reported. these occur when using option -m to normalize read to reads per million.

Version 1.1

Added option -m, which counts each read, instead of 1, as (1/(n mapped reads) * 1E6) [AKA reads per million].

Version 1.0

Ended internal use of samtools depth to avoid the sneaky max limit of 8000 reads. Runs a little slower now but depths are reported accurately.

Version 0.2

• Fixed bad bug that was causing any runs using option -l and/or -L to fail.

Version 0.1

First release.