Changelog
0.6.0
- Map .nex extension to NEXUS-format (–alphabet must be specified if writing)
- Use reservoir sampling in --sample selector (lower memory use)
- Support specifying negative indices to --cut [GH-33]
- Optionally allow invalid codons in backtrans-align [GH-34]
- Map .fq extension to FASTQ format
- Optional multithreaded I/O in info [GH-36]
- Print sequence name on length mismatch in backtrans-align [GH-37]
- Support for + and - in head and tail to mimick Linux head and tail commands.
- Fix scoring for mixed-case sequences in primer-trim.
- Fix bug in primer-trim - failed when sequence had multiple 5’ gaps compared to the primer.
- Clarify documentation and fix bug in convert/mogrify --pattern-replace [GH-39]
- Support for gzip files in seqmagick convert --sort
0.5.0
- Change seqmagick extract-ids --source-format to --input-format to match
other commands (GH-29)
- Support gzip- and bzip2-compressed inputs and outputs for most commands (GH-30)
- Change default input format for sff to sff-trim, which respects the
clipping locations embedded in each sequence record.
- Add --details-out option to seqmagick quality-filter, which writes
details on each read processed.
- Match barcode/primer seqmagick quality-filter against a trie; allows
per-specimen barcodes.
- Remove --failure-out option from seqmagick quality-filter. See --details-out
- Raise an error if number of codons does not match number of amino acids in
seqmagick backtrans-align
- Add --sample subcommand (GH-31)
0.4.0
- Fix bug in --squeeze
- More informative messages in seqmagick primer-trim
- Added --alphabet flag to allow writing NEXUS (GH-23)
- Exiting without error on SIGPIPE in extract-ids, info (GH-17)
- Ambiguities are translated as ‘X’ in –translate (GH-16)
- Allowing ‘.’ or ‘-‘ as gap character (GH-18)
- --name-prefix and --name-suffix no longer create a mangled description (GH-19)
- Files owned by another user can be mogrified, as long as they are group writeable (GH-14)
- Add backtrans-align subcommand, which maps unaligned nucleotides onto a
protein alignment (GH-20)
- Allow FASTQ as input to quality-filter
- Significantly expand functionality of quality-filter: identify and trim
barcodes/primers; report detailed failure information.
- Cleanup, additional tests
- Add --drop filter to convert and mogrify (GH-24)
- Apply current umask when creating files (GH-26)
- Support stdin in seqmagick info (GH-27)
- Support translating ambiguous nucleotides, if codon translation is unambiguous
0.3.1
- Fix bug in quality-filter MinLengthFilter
- Case consistency in seqmagick
0.3.0
- Internal reorganization - transformations are converted to partial functions,
then applied.
- Argument order now affects order of tranformation application.
- Change default output format to ‘align’ for TTYs in seqmagick info
- Add BioPython as dependency (closes GH-7)
- Add primer-trim subcommand
- Add option to apply custom function(s) to sequences
- Add new filtering options: --squeeze-threshold, --min-ungapped-length
--include-from-file --exclude-from-file
- Removed seqmagick muscle
- Added new subcommand quality-filter
- Added new subcommand extract-ids (closes GH-13)
- Allow use of ‘-‘ to indicate stdin / stdout (closes GH-11)
- Add mapping from .phyx to phylip-relaxed (targeted for BioPython 1.58)
0.2.0
- Refactoring
- Added hyphenation to multi-word command line options (e.g.
--deduplicatetaxa -> --deduplicate-taxa)
- Add support for .needle, .sff formats
- Close GH-4