What’s New (History)¶

Post Version 1.0.1¶

User-visible improvements¶

ZSTD compression is available for output and intermediate files use it for reduced temporary space usage (and possibly faster processing).
The countfile now reorders its input if it is not ordered. This is necessary for correct usage.
Added include_fragments option to orf_find().
More flexible loading of functional_map arguments in count to accept multiple comment lines at the top of the file as produced by eggnog-mapper.
Faster check for column headers in functional_map argument to count() function: now it is performed as soon as possible (including at the top of the script if the arguments are literal strings), thus NGLess can fail faster.
Added sense argument to the count function, generalizing the previous strand argument (which is deprecated). Whereas before it was only possible to consider features either to be present on both strands or only on the strand to which they are annotated, now it is also possible to consider them present only on the opposite strand (which is necessary for some strand-specific protocols as they produce the opposite strand).
Added interleaved argument to fastq

Version 1.0.1¶

This is a bugfix release and results should not change.

Bugfixes¶

Fix bug with external modules and multiple fastQ inputs.
Fix bug with resaving input files where the original file was sometimes moved (thus removing it).

Version 1.0¶

User-visible improvements¶

The handling of multiple annotations in count (i.e., when the user requests multiple features and/or subfeatures) has changed. The previous model caused a few issues (#63, but also mixing with collect(). Unfortunately, this means that scripts asking for the old behaviour in their version declaration are no longer supported if they use multiple features.

Version 0.11¶

Released March 15 2019 (0.11.0) and March 21 2019 (0.11.1).

Version 0.11.0 used ZStdandard compression, which was not reliable (the official haskell zstd wrapper has issues). Thus, it was removed in v0.11.1. Using v0.11.0 is not recommended.

User-visible improvements¶

Module samtools (version 0.1) now includes samtools_view
Add –verbose flag to check-install mode (ngless –check-install –verbose)
Add early checks for input files in more situations (#33)
Support compression in collect() output (#42)
Add smoothtrim() function

Bugfixes¶

Fix bug with orf_find & prots_out argument
Fix bug in garbage collection where intermediate files were often left on disk for far longer than necessary.
Fix CIGAR (#92) for select() blocks

Internal improvements¶

Switched to diagrams package for plotting. This should make building easier as cairo was often a complicated dependency.
Update to LTS-13 (GHC 8.6)
Update minimap2 version to 2.14
Call bwa/minimap2 with interleaved fastq files. This avoids calling it twice (which would mean that the indices were read twice).
Avoid leaving open file descriptors after FastQ encoding detection
Tar extraction uses much less memory now (#77)

Version 0.10.0¶

Released Nov 12 2018

Bugfixes¶

Fixed bug where header was printed even when STDOUT was used
Fix to lock1’s return value when used with paths (#68 - reopen)
Fixed bug where writing interleaved FastQ to STDOUT did not work as expected
Fix saving fastq sets with –subsample (issue #85)
Fix (hypothetical) case where the two mate files have different FastQ encodings

User-visible improvements¶

samtools_sort() now accepts by={name} to sort by read name
Add __extra_megahit_args to assemble() (issue #86)
arg1 in external modules is no longer always treated as a path
Added expand_searchdir to external modules API (issue #56)
Support _F/_R suffixes for forward/reverse in load_mocat_sample
Better error messages when version is mis-specified
Support NO_COLOR standard: when NO_COLOR is present in the environment, print no colours.
Always check output file writability (issue #91)
paired() now accepts encoding argument (it was documented to, but mis-implemented)

Internal improvements¶

NGLess now pre-emptively garbage collects files when they are no longer needed (issue #79)

Version 0.9.1¶

Released July 17th 2018

Added NGLess preprint citation

Version 0.9¶

Released July 12th 2018

User-visible improvements¶

Added allbest() method to MappedRead.
NGLess will issue a warning before overwriting an existing file.
Output directory contains PNG files with basic QC stats
Added modules for gut gene catalogs of mouse, pig, and dog
Updated the integrated gene catalog

Internal improvements¶

All lock files now are continuously “touched” (i.e., their modification time is updated every 10 minutes). This makes it easier to discover stale lock files.
The automated downloading of builtin references now uses versioned URLs, so that, in the future, we can change them without breaking backwards compatibility.

Version 0.8.1¶

Released June 5th 2018

This is a minor release and upgrading is recommended.

Bugfixes¶

Fix for systems with non-working locale installations
Much faster collect calls
Fixed lock1 when used with full paths (see issue #68)
Fix expansion of searchpath with external modules (see issue #56)

Version 0.8¶

Released May 6th 2018

Incompatible changes¶

Added an extra field to the FastQ statistics, with the fraction of basepairs that are not ATCG. This means that uses of qcstats must use an up-to-date version declaration.
In certain cases (see below), the output of count when using a GFF will change.

User-visible improvements¶

Better handling of multiple features in a GFF. For example, using a GFF containing “gene_name=nameA,nameB” would result in:
```
  nameA,nameB    1

Now the same results in::

  nameA          1
  nameB          1
```
This follows after https://git.io/vpagq and the case of Parent=AF2312,AB2812,abc-3

Support for minimap2 as alternative mapper. Import the minimap2 module and specify the mapper when calling map. For example:

ngless '0.8'
import "minimap2" version "1.0"

input = paired('sample.1.fq', 'sample.2.fq', singles='sample.singles.fq')
mapped = map(input, fafile='ref.fna', mapper='minimap2')
write(mapped, ofile='output.sam')

Added the </> operator. This can be used to concatenate filepaths. p0 </> p1 is short for p0 + "/" + p1 (except that it avoids double forward slashes).
Fixed a bug in select where in some edge cases, the sequence would be incorrectly omitted from the result. Given that this is a rare case, if a version prior to 0.8 is specified in the version header, the old behaviour is emulated.
Added bzip2 support to write.
Added reference argument to count.

Bug fixes¶

Fix writing multiple compressed Fastq outputs.
Fix corner case in select <Functions.html#select>__. Previously, it was possible that some sequences were wrongly removed from the output.

Internal improvements¶

Faster collect()
Faster FastQ processing
Updated to bwa 0.7.17
External modules now call their init functions with a lock
Updated library collection to LTS-11.7

Version 0.7.1¶

Released Mar 17 2018

Improves memory usage in count() and the use the when-true flag in external modules.

Version 0.7¶

Released Mar 7 2018

New functionality in NGLess language¶

Added max_trim argument to filter method of MappedReadSet.
Support saving compressed SAM files
Support for saving interleaved FastQ files
Compute number Basepairs in FastQ stats
Add headers argument to samfile function

Bug fixes¶

Fix count’s mode {intersection_strict} to no longer behave as {union}
Fix as_reads() for single-end reads
Fix select() corner case

In addition, this release also improves both speed and memory usage.

Version 0.6¶

Released Nov 29 2017

Behavioural changes¶

Changed include_m1 default in count() function to True

New functionality in NGLess language¶

Added orf_find function (implemented through Prodigal) for open reading frame (ORF) predition
Add qcstats() function to retrieve the computed QC stats.
Added reference alias for a more human readable name
Updated builtin referenced to include latest releases of assemblies

New functionality in NGLess tools¶

Add –index-path functionality to define where to write indices.
Allow citations as key in external modules (generally better citations information)
Use multiple threads in SAM->BAM conversion
Better error checking/script validation

Bug fixes¶

Output preprocessed FQ statistics (had been erroneously removed)
Fix –strict-threads command-line option spelling
Version embedded megahit binary
Fixed inconsistency between reference identifiers and underlying files

Version 0.5.1¶

Released Nov 2 2017

Fixed some build issues

Version 0.5¶

Released Nov 1 2017

First release supporting all basic functionality.