What’s New (History)

Development version

Version 0.9.1

Released July 17th 2018

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 searchdir 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.