Hi, version 1.7 of samtools and htslib are available and version 1.6 of bcftools. see http://www.htslib.org/download/ Could you please update the ebuilds? sci-libs/htslib sci-biology/samtools sci-biology/bcftools Thanking you!
bcftools should be kept in sync, therefore there is now bcftools-1.7 out too. BCFtools 1.7 is now available from GitHub and SourceForge (Samtools and HTSlib 1.7 were previously released on 26th January). https://sourceforge.net/projects/samtools/ https://github.com/samtools/bcftools/releases/tag/1.7 The main changes are listed below: ------------------------------------------------------------------------------ bcftools - changes v1.7 ------------------------------------------------------------------------------ * `-i, -e` filtering: Major revamp, improved filtering by FORMAT fields and missing values. New GT=ref,alt,mis etc keywords, check the documentation for details. * `query`: Only matching expression are printed when both the -f and -i/-e expressions contain genotype fields. Note that this changes the original behaviour. Previously all samples were output when one matching sample was found. This functionality can be achieved by pre-filtering with view and then streaming to query. Compare bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf and bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' * `annotate`: New -k, --keep-sites option * `consensus`: Fix --iupac-codes output * `csq`: Homs always considered phased and other fixes * `norm`: Make `-c none` work and remove `query -c` * `roh`: Fix errors in the RG output * `stats`: Allow IUPAC ambiguity codes in the reference file; report the number of missing genotypes * `+fill-tags`: Add ExcHet annotation * `+setGt`: Fix bug in binom.test calculation, previously it worked only for nAlt<nRef! * `+split`: New plugin to split a multi-sample file into single-sample files in one go * Improve python3 compatibility in plotting scripts
Feel free to send in a PR.
1.8 is out, and 1.8 can only be added once pysam is updated against 1.8
version 1.9 is out PR for in science overlay: https://github.com/gentoo/sci/pull/875
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59ee040ec29f25e981534026d9be99b4ca36b458 commit 59ee040ec29f25e981534026d9be99b4ca36b458 Author: David Seifert <soap@gentoo.org> AuthorDate: 2018-10-28 20:24:40 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2018-10-28 20:24:40 +0000 sci-biology/bcftools: Version bump to 1.9 Closes: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert <soap@gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11 sci-biology/bcftools/Manifest | 1 + sci-biology/bcftools/bcftools-1.9.ebuild | 47 ++++++++++++++++++++++ .../bcftools/files/bcftools-1.9-fix-shebangs.patch | 8 ++++ 3 files changed, 56 insertions(+) Additionally, it has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=18d496c1b4022e892aae9fcf3350b302b34357ed commit 18d496c1b4022e892aae9fcf3350b302b34357ed Author: David Seifert <soap@gentoo.org> AuthorDate: 2018-10-28 20:24:37 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2018-10-28 20:24:37 +0000 sci-biology/samtools: Version bump to 1.9 Bug: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert <soap@gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11 sci-biology/samtools/Manifest | 1 + sci-biology/samtools/samtools-1.9.ebuild | 52 ++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=85fad26e8efb7e2fc01de49e59a0d7e0b210c5bc commit 85fad26e8efb7e2fc01de49e59a0d7e0b210c5bc Author: David Seifert <soap@gentoo.org> AuthorDate: 2018-10-28 20:24:33 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2018-10-28 20:24:33 +0000 sci-libs/htslib: Version bump to 1.9 Bug: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert <soap@gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11 sci-libs/htslib/Manifest | 1 + sci-libs/htslib/htslib-1.9.ebuild | 45 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+)
There are a few breakages with this update: 1. sci-biology/pysam-0.12.0.1 blocks the update, needs updating to 0.15.1 2. samtools-1.9 ebuild no longer installs headers nor properly installs libbam.so (as in samtools-1.5) needed for sci-biology/augustus 3. sci-biology/augustus-3.3 rebuilds because of libbam.so, and fails because dependencies of big2wig have moved. Might as well update to 3.3.2 while you're at it.
