List of language changes

Every NGLess script declares a language version on its first line. This page documents the changes in behaviour introduced by each version so that you can understand what a script written for an older version expected.

Note that, in 1.6.0, NGLess supports exactly one language version, 1.6. Older versions are documented here for reference, but scripts must be updated to declare ngless "1.6" to run.

NGLess 1.6

• NGLess is now based on a Rust implementation (previous versions were written in Haskell). Update your version declaration to ngless "1.6"; earlier versions are no longer supported.

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.

• write() returns the filename used. Before this, it returned nothing.

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.

• countfile reorders its input if necessary.

• The count function now accepts multiple lines of comments at the top of its functional_map arguments.

• count() uses the sense argument for strand-specific data. Older scripts may use the deprecated boolean strand argument, where strand=True maps to sense={sense} and strand=False maps to sense={both}.

• Older Haskell releases of the mocat module exposed coord_file_to_gtf() to convert MOCAT .coord files to GTF. This helper is not part of the current Rust standard module surface.

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|:
    ...