NGLess-1.4.0: ChangeLog
Version 1.4.0 2022-05-30 by luispedro
* Add --trace argument to all modes
* Update --create-reference-pack mode to newer format (previous version worked, but
users still had to recreate indices after downloading, negating some of
the benefits
* Update --install-reference-data mode to download latest version (#107)
* Update --create-reference-pack mode to download latest version (#108)
* Do not fail when merging empty files (#113)
* write() returns the filename used
* Switch to tasty test framework
* Update to LTS-19
* write() uses multiple threads to write multiple FQ files
* Use binaries from path (not self installed)
* Better error message when parsing misformed FastQ files
* Overhall building infrastructure to use haskell.nix and build
dependencies with nix
* Update megahit version
* Added GMGC to builtin Modules
* Make `--print-path minimap2` work correctly
Version 1.3.0 2021-01-28 by luispedro
* Validate count() headers on --validate-only
* Better error message if the user attempts to use the non-existent <\>
operator (suggest </>)
* Add min-ngless-version field for modules
* Add early check that block assignments are always to block variables
* Use ZStd compression for temporary files from preprocess()
* Correctly handle subpaths in samples for collect (fixes #141)
* Add to_string() to int and double types (partially fixes #78 & fixes #81)
* Add read_int() and read_double() functions (fixes #78)
Version 1.2.0 2020-07-12 by luispedro
* Add load_fastq_directory to builtin functions
* Better messages when using `lock1`
* Enable specifying *all* module resources by URL with download on first
use
* Fix CIGAR reinjection bug
* Remove old motus/specI modules
* No longer ship JS libraries (also do not expand them in-place)
Version 1.1.0 2020-01-25 by luispedro
* Reintroduce zstd compression (after fixes upstream)
* Fix CIGAR interpretation (#109) occurring when I is present
* Call bwa mem so that it behaves in a deterministic way (independently of
the number of threads used)
* Add `include_fragments` option to orf_find
* Add early check for column headers in `count()`
* Update to LTS-14.1 (fixes #116)
* Add ``sense`` argument to `count()`
* Add line numbers to FastQ parsing errors
* Fix __extra_args argument in map()
* Add `discard_singles` function
* Add `interleaved` option to fastq()
* `load_mocat_sample` now fails if `pair.2` exists but `pair.1` doesn't
Version 1.0.1 2019-07-05 by luispedro
* 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 1.0.0 2019-04-24 by luispedro
* Fix multiple features usage (#63)
* Update minimap2/megahit to latest versions
Version 0.11.1 2019-03-21 by luispedro
* Fix reinjectSequence in select() call with blocks
* Remove zstd compression
* Fix SAM order switching in select() call with blocks (#105)
* Compress SAM files after select() calls
Version 0.11.0 2019-03-15 by luispedro
* Switch to diagrams package for plotting
* Update minimap2 version to 2.14
* Module samtools (version 0.1) now includes samtools_view
* Update to LTS-13 (GHC 8.6)
* Fix bug with orf_find & prots_out argument
* Call bwa/minimap2 with interleaved fastq files
* Add --verbose flag to check-install mode
* Avoid leaving open file descriptors after FastQ encoding detection
* Fix bug in garbage collection
* Compress intermediate SAM files (#22)
* Tar extraction uses much less memory (#77)
* Add early checks for input files in more situations (#33)
* Support compression in collect() output (#42)
* Fix CIGAR (#92) for select() blocks
* Add smoothtrim function
* Fix lock1()/collect() use with --subsample
* Fix compression/decompression when calling external modules
Version 0.10.0 2018-11-12 by luispedro
* Fix to lock1's return value when used with paths (#68 - reopen)
* Support _F/_R suffixes for forward/reverse in load_mocat_sample
* samtools_sort() now accepts by={name} to sort by read name
* Fixed bug where header was printed even when STDOUT was used
* Fixed bug where writing interleaved FastQ to STDOUT did not work as
expected
* Indices created by bwa and minimap2 are now versioned
* arg1 in external modules is no longer always treated as a path
* Added expand_searchpath to external modules API (closes #56)
* Fixed bug where detection of Fastq encoding was not performed on the second pair
* Fix saving fastq sets with --subsample (issue #85)
* Add __extra_megahit_args to assemble() (issue #86)
* Better error message when user mis-specifies the ngless version string
(issue #84)
* Support NO_COLOR environment variable (issue #83)
* Garbage collection for temporary files (issue #79)
* Rename --search-dir to --search-path for consistency with other API
* Fix corner case with select() producing incorrect CIGAR strings (#92)
* Always check output file writability (#91)
* Make paired() accept encoding argument
Version 0.9.1 2018-07-17 by luispedro
* Add biorxiv citation
Version 0.9.0 2018-07-12 by luispedro
* 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
Version 0.8.1 2018-06-05 by luispedro
* Update to LTS-11.12 (for faster conduit-algorithms used in collect())
* Add fallback for character encoding on systems with bad locale support
* Fixed lock1 when used with paths (#68)
* Fixed expansion of searchdir with external modules (#56)
Version 0.8.0 2018-05-06 by luispedro
* Add minimap2 support as alternative mapper
* Faster collect()
* Fix writing of multiple compressed files to uncompressed format
* Add `n_to_zero_quality` method for short reads
* Add </> operator for path manipulation
* Fix bug in select (corner case where sequences would be missing from
output)
* Add non-ATCG fraction field to FastQ statistics
* Add reference argument to count()
* GFF based counting now expands multi-value sub-features
* Update to bwa 0.7.17
Version 0.7.1 2018-03-17 by luispedro
* Fix memory leak in count()
* Fix when-true flag usage with external modules
Version 0.7.0 2018-03-07 by luispedro
* Add 'failed' files to parallel lock1()
* Add `max_trim` argument to MappedReadSet.filter()
* Support saving compressed SAM files
* Much faster select() implementation with a block
* Fix count's mode {intersection_strict} to no longer behave as {union}
* Support for saving interleaved FastQ files
* Lower memory usage
* More conservative SAM merging in split mode
* Compute #Basepairs in FastQ stats
* Fix as_reads() for single-end reads
* Add headers argument to samfile()
* For more situations, avoid intermediate copies in count()
* Much improved memory and speed performance of count()
* Fix select() corner case
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()
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
Version 0.5.1 2017-11-02 by luispedro
* Fix building step (static compilation)
Version 0.5.0 2017-11-01 by luispedro
* First release supporting all basic functionality.