Release 1.0.1

This is a bugfix release for version 1.0: upgrading is recommended and no changes in behaviour are expected (except in situations where NGLess used to fail and will now produce the correct result).

Release 1.0.0

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.

Release 0.11.1

Release 0.11.1 fixes issues in 0.11.0 (which should not be used).

Release 0.11

User-visible improvements since version 0.10

• 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 since version 0.10

• 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 since version 0.10

• 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)

NGLess 0.11.0

Release 0.11.0

Please use version 0.11.1 as this release introduced an important bug due to the unreliability of zstandard compression (as it manifests itself only in a small subset of inputs, it it hard to test for). The bug manifests itself in ngless exiting with an internal error. Thus, if you got results with v0.11.0, they can be trusted.

A collection of several bugfixes and performance improvements over the last few months.

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
• Compress intermediate SAM files. In some situations this should even speed up the process as Zstandard compression is used and the process was often IO bound (#22)
• Tar extraction uses much less memory now (#77)

Release 0.9.1

Adds biorxiv preprint link.

Release 0.9.0

Many small improvements:

• Add allbest() method to mappedreads
• Output FastQ quality graphs as PNGs
• Added MouseGutCatalog module
• Added DogGutGeneCatalog module
• Added PigGeneCatalog module
• Added reference genome for Sus scrofa (pig)
• Update IGC module to 0.9
• Continuously update mtime on all lock files
• Warn when overwriting files
• Version automatically downloaded reference URLs

0.6.1

Bug fixes:

• make install works now
• index splitting works with --index-path

Full ChangeLog

Version 0.6.1 2017-12-10 by luispedro
    * Add --check-install mode
    * Fix streaming short read QC (performance regression)
    * Better error message in readlines() when file opening fails
    * Compute statistics after select()

0.6.0

Big new changes are orf_find(), qcstats() [and generally much better
statistics], and the low memory mode.

Full ChangeLog:

Version 0.6.0 2017-11-29 by luispedro
* Add `orf_find` function (implemented through Prodigal)
* Add qcstats() function
* Output preprocessed FQ statistics (had been erroneously removed)
* Fix --strict-threads command-line option spelling
* Use multiple threads in SAM->BAM conversion
* Change include_m1 default in count() function to True
* Add --index-path functionality to define where to write indices (issue #47)
* Allow `citations` as key in external modules
* Better citations information
* Better error checking/script validation
* Added reference alias for a more human readable name
* Version embedded megahit binary
* Updated builtin referenced to include latest releases of assemblies
* Fixed inconsistency between reference identifiers and underlying files

See the release notes for more information.

0.5.1

Fixes compilation issues in version 0.5.0 (no functional changes).

Release 0.5.0

First tagged release.

This version supports all basic NGLess functionality.