List of backwards compatibility fixes

As NGLess uses a version declaration string at the top of script means that NGLess can change its behaviour depending on the version used in the script.

This page documents the fixes that are currently implemented.

NGLess 1.4

• The old motus module (which supports only motus version 1, which is a reference from 2013) is not supported any more. Upgrade to the new external motus module if possible.

NGLess 1.1

• The way that CIGAR sequence lengths are computed has changed to match samtools. This implies that the computation of min_match_size and min_identity_pc have slightly changed.
• Starting in NGLess 1.1, countfile reorders its input if necessary.
• The count function now accepts multiple lines of comments at the top of its functional_map arguments

NGLess 0.8

• The select handles a strange corner case differently (it was arguably wrong before, but affects very few reads).

NGLess 0.6

• The count function now defaults to include_minus1 being true.

NGLess 0.5

• The preprocess function now modifies its argument. Older code using

preprocess(input) using |r|:
    ...

is automatically treated as:

input = preprocess(input) using |r|:
    ...