What’s New (History)

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.