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
andmin_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 itsfunctional_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 toinclude_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|:
...