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adam 066be082ec py-cutadapt: updated to 3.5 
v3.5 (2021-09-29)
-----------------

* :issue:`555`: Add support for dumping statistics in JSON format using ``--json``.
* :issue:`541`: Add a "Read fate breakdown" section heading to the report, and also
  add statistics for reads discarded because of ``--discard-untrimmed`` and
  ``--discard-trimmed``. With this, the numbers in that section should add up to 100%.
* Add option ``-Q``, which allows to specify a quality-trimming threshold for R2 that is
  different from the one for R1.
* :issue:`567`: Add ``noindels`` adapter-trimming parameter. You can now write
  ``-a "ADAPTER;noindels"`` to disallow indels for a single adapter only.
* :issue:`570`: Fix ``--pair-adapters`` not finding some pairs when reads contain
  more than one adapter.
* :issue:`524`: Fix a memory leak when using ``--info-file`` with multiple cores.
* :issue:`559`: Fix adjacent base statistics not being shown for linked adapters.
2022-01-17 09:03:10 +00:00
..
ad2vcf biology/ad2vcf: Update to 0.1.4 2021-12-14 19:02:21 +00:00
arka biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
azara revbump for icu and libffi 2021-12-08 16:01:42 +00:00
bcftools biology/bcftools: Update to 1.14 2021-12-17 15:14:35 +00:00
beagle biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
bedtools biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
biolibc biology/biolibc: Update to 0.2.1 2021-12-14 18:58:56 +00:00
biolibc-tools biology/biolibc-tools: Update to 0.1.1 2021-12-14 19:05:39 +00:00
bioperl biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
bodr revbump for icu and libffi 2021-12-08 16:01:42 +00:00
bowtie2 biology/bowtie2: Update to 2.4.4 2021-12-17 15:25:20 +00:00
bwa biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
canu *: Recursive revbump from boost 1.78.0 2022-01-10 01:46:21 +00:00
cdhit biology/cdhit: Update to 4.8.1 2021-12-17 17:57:55 +00:00
chemical-mime-data biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
chemtool revbump for icu and libffi 2021-12-08 16:01:42 +00:00
clustalw biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
coalesce biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
coordgenlibs *: Recursive revbump from boost 1.78.0 2022-01-10 01:46:21 +00:00
fastDNAml biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
fastp biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
fastqc biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
filter-fastq biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
fluctuate biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
gabedit revbump for icu and libffi 2021-12-08 16:01:42 +00:00
generand biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
genesplicer biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
glimmer biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
gnome-chemistry-utils revbump for icu and libffi 2021-12-08 16:01:42 +00:00
gp biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
gromacs revbump for icu and libffi 2021-12-08 16:01:42 +00:00
hisat2 biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
hmmer biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
htslib biology/htslib: Update to 1.14 2021-12-17 15:01:27 +00:00
igv biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
kallisto biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
lucy biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
maeparser *: Recursive revbump from boost 1.78.0 2022-01-10 01:46:21 +00:00
miniasm biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
minimap2 biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
molsketch biology/molsketch: fix broken build 2022-01-11 16:45:09 +00:00
mopac biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
mpqc biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
mummer biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
ncbi-blast+ revbump for icu and libffi 2021-12-08 16:01:42 +00:00
nut biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
openbabel *: Recursive revbump from boost 1.78.0 2022-01-10 01:46:21 +00:00
p5-Bio-ASN1-EntrezGene biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
pdbalign biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
peak-classifier biology/peak-classifier: Update to 0.1.2 2021-12-14 19:08:11 +00:00
phylip biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
plink biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
plinkseq *: Revbump for protobuf-3.19.0 2021-11-11 12:02:46 +00:00
primer3 biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
profit biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
puzzle biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
py-biopython *: bump PKGREVISION for egg.mk users 2022-01-04 20:52:30 +00:00
py-cutadapt py-cutadapt: updated to 3.5 2022-01-17 09:03:10 +00:00
py-dnaio *: bump PKGREVISION for egg.mk users 2022-01-04 20:52:30 +00:00
py-mol py-mol: convert to egg.mk 2022-01-10 18:46:54 +00:00
py-pydicom python: egg.mk: add USE_PKG_RESOURCES flag 2022-01-05 15:40:56 +00:00
R-popbio biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
racon biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
rasmol biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
samtools biology/samtools: Update to 1.14 2021-12-17 15:10:06 +00:00
sewer biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
stacks biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
stride biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
trimmomatic biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
vcf-split biology/vcf-split: Update to 0.1.3.3 2021-12-14 19:10:43 +00:00
vcf2hap biology/vcf2hap: Update to 0.1.4 2021-12-14 19:12:10 +00:00
vsearch biology/vsearch: Update to 2.18.0 2021-12-17 19:20:44 +00:00
xylem biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
Makefile biology/Makefile: Add biolibc-tools 2021-08-31 15:56:42 +00:00