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.
- The old
motusmodule (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.
- The way that CIGAR sequence lengths are computed has changed to match
samtools. This implies that the computation of
min_identity_pchave slightly changed.
- Starting in NGLess 1.1,
countfilereorders its input if necessary.
countfunction now accepts multiple lines of comments at the top of its
selecthandles a strange corner case differently (it was arguably wrong before, but affects very few reads).
countfunction now defaults to
preprocessfunction now modifies its argument. Older code using
preprocess(input) using |r|: ...
is automatically treated as:
input = preprocess(input) using |r|: ...