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pkgsrc/biology
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adam 92bc32e2ea htslib: updated to 1.15.1 
1.15.1

Security fix: Fixed broken error reporting in the sam_cap_mapq() function, due to a missing hts_log() parameter. Prior to this fix it was possible to abuse the log message format string by passing a specially crafted alignment record to this function.

HTSlib now uses libhtscodecs release 1.2.2. This fixes a number of bugs where invalid compressed data could trigger usage of uninitialised values.

Fixed excessive memory used by multi-threaded SAM output on long reads.

Fixed a bug where tabix would misinterpret region specifiers starting at position 0. It will also now warn if the file being indexed is supposed to be 1-based but has positions less than or equal to 0.

The VCF header parser will now issue a warning if it finds an INFO header with Type=Flag but Number not equal to 0. It will also ignore the incorrect Number so the flag can be used.
2022-07-05 11:00:16 +00:00
..
ad2vcf biology/ad2vcf: Update to 0.1.6 2022-06-11 19:48:32 +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 *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +00:00
beagle biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
bedtools *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +00:00
biolibc biology/biolibc: Update to 0.2.3 2022-06-11 19:42:39 +00:00
biolibc-tools biology/biolibc-tools: Update to 0.1.3 2022-06-11 19:44:45 +00:00
bioperl *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
bodr *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
bowtie2 *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +00:00
bwa *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
canu *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
cdhit *: recursive bump for perl 5.36 2022-06-28 11:30:51 +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 *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
fastx-toolkit *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
filter-fastq *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +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 *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
gp biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
gromacs *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
hisat2 *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +00:00
hmmer biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
htslib htslib: updated to 1.15.1 2022-07-05 11:00:16 +00:00
igv biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
kallisto biology/kallisto: Update to 0.48.0 2022-02-27 01:57:27 +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/minimap2) Updated 2.18 to 2.24 2022-03-13 08:05:07 +00:00
molsketch revbump for textproc/icu update 2022-04-18 19:09:40 +00:00
mopac biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
mpqc *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
mummer *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
ncbi-blast+ *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +00:00
nut biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
openbabel revbump for textproc/icu update 2022-04-18 19:09:40 +00:00
p5-Bio-ASN1-EntrezGene *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
pdbalign biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
peak-classifier *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +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 devel/protobuf 2022-04-03 18:50:16 +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 py-biopython: update to 1.79. 2022-02-17 10:44:49 +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-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 *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +00:00
sewer biology: Replace RMD160 checksums with BLAKE2s checksums 2021-10-26 10:03:36 +00:00
stacks *: Revbump packages that use Python at runtime without a PKGNAME prefix 2022-06-30 11:18:01 +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 0.1.5 2022-06-11 19:46:43 +00:00
vcf2hap biology/vcf2hap: Update to 0.1.6 2022-06-11 19:50:59 +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 fastx-toolkit 2022-04-05 18:49:29 +00:00