Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data. The selection of trimming steps and their
associated parameters are supplied on the command line. It works with FASTQ
(using phred + 33 or phred + 64 quality scores, depending on the Illumina
pipeline used), either uncompressed or gzipp'ed FASTQ.
Performing substitutions during post-patch breaks tools such as mkpatches,
making it very difficult to regenerate correct patches after making changes,
and often leading to substituted string replacements being committed.
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
OK wiz@
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
between sequences. The program compares nucleotide or protein sequences to
sequence databases and calculates the statistical significance of matches.
BLAST can be used to infer functional and evolutionary relationships between
sequences as well as help identify members of gene families.
OK wiz@
The actual fix as been done by "pkglint -F */*/buildlink3.mk", and was
reviewed manually.
There are some .include lines that still are indented with zero spaces
although the surrounding .if is indented. This is existing practice.
Unsorted entries in PLIST files have generated a pkglint warning for at
least 12 years. Somewhat more recently, pkglint has learned to sort
PLIST files automatically. Since pkglint 5.4.23, the sorting is only
done in obvious, simple cases. These have been applied by running:
pkglint -Cnone,PLIST -Wnone,plist-sort -r -F
This has been a pkglint warning for several years now, and pkglint can even
fix it automatically. And it did for this commit.
Only in lang/mercury, two passes of autofixing were necessary because there
were nested variables.
1.72 2016-09-02 06:50:53-05:00 America/Chicago
* Full release (no changes from 1.71 beyond version)
1.71 2016-09-01 22:57:25-05:00 America/Chicago (TRIAL RELEASE)
* Minor bump for impending BioPerl 1.7 release.
* #2 : 'Unescaped left brace in regex is deprecated' with newer versions of perl
fixed [fjossandon]
Add p5-Text-Diff as test dependency.
1.7.2 - "Entebbe"
[Bugs]
* #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
* #245 - Code coverage fixes [zmughal,cjfields]
* #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
* #238 - Use a Travis cron job for network tests [zmughal,cjfields]
* #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
* #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
* #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
* #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
* #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
* #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
* #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
* #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
[Code changes]
* PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
MASTER_SITES= site1 \
site2
style continuation lines to be simple repeated
MASTER_SITES+= site1
MASTER_SITES+= site2
lines. As previewed on tech-pkg. With thanks to rillig for fixing pkglint
accordingly.
Upstream changes:
1.7.1 - "Election"
[Bugs]
* Minor release to incorporate fix for CPAN indexing, which
prevented proper updates [cjfields]
* Fix problem in managing Target attribute for gff3 [Jukes34]
* Minor bug fixes related to NCBI HTTPS support [cjfields]
1.7.0 - "Disney"
[New site]
* We have migrated to Github Pages. This was actually planned, but the
recent OBF server compromise forced our hand.
Brian Osborne [bosborne] took this under his wing to move docs and has
done a tremendous amount of work formatting the site and working out some
of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
Cantalupo and Franscison Ossandon also helped. Kudos!!
* Similarly, the official issue tracker is now Github Issues. This has
been updated in the relevant documentation bits (we hope!)
[Code changes]
* Previously deprecated modules removed
* Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
* Bio::DB::SeqHound has been removed due to the service no longer being
available
* Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
reasons due to the server no longer having a valid cert
* Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
* Bio::Coordinate, Bio::SearchIO::blastxml,
Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
added on CPAN
[New features]
* Docker instances of tagged releases are available! [hlapp]
* NCBI HTTPS support [mjohnson and others]
* Bio::SearchIO::infernal
- Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
* Bio::Search::HSP::ModelHSP
- Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
reports [pcantalupo]
* Bio::Search::Result::INFERNALResult
- Added new module to represent features of Infernal reports [pcantalupo]
* Bio::DB::Taxonomy SQLite option [cjfields]
* WrapperBase quoted option values [majensen]
* Various documentation fixes and updates [bosborne]
[Bug Fixes]
* Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
* Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
* NeXML parser fixes [fjossandon]
* Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
* RT 103272 : SeqFeature database deletion skipped features with a decimal -
Joshua Fortriede (Xenbase)
* RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
* Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
* Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
* Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
* Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
* Issue #84: EMBL format wrapping problem [nyamned]
* Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
* Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
or compiled C code (when Inline::C is installed) [rocky]
* Fix various Bio::Tools::Analysis remote server config problems [cjfields]
* Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
* Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
* For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
to be consistent with "$hit->bits" behaviour [fjossandon]
* Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
aminoacids made "next_seq" confused and broke the parser [fjossandon]
* Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
to "complement(join(A..B,C..D))" [fjossandon]
* For the many many many fixes that weren't mentioned - blame the release guy!
