Michael R. Crusoe pushed to branch master at Debian Med / kallisto
Commits: e76b8f4a by Michael R. Crusoe at 2019-12-25T11:06:36Z routine-update: Ready to upload to unstable - - - - - 2a885325 by Michael R. Crusoe at 2019-12-25T11:08:43Z kallisto-examples: Multi-Arch: foreign - - - - - 0faced6e by Michael R. Crusoe at 2019-12-25T11:11:13Z fix typo - - - - - 7f4ecc02 by Michael R. Crusoe at 2019-12-25T11:22:12Z htslib1.3 fix - - - - - 6 changed files: - debian/changelog - debian/control - debian/copyright - + debian/patches/htslib1.3 - debian/patches/series - + debian/patches/spelling Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +kallisto (0.46.1+dfsg-2) unstable; urgency=medium + + * Team upload. + * mark kallisto-examples as Multi-Arch: foreign + * debian/patches/spelling: fix typo + * debian/patches/htslib1.3: use kseq.h from htslib, not the bundled version + + -- Michael R. Crusoe <[email protected]> Wed, 25 Dec 2019 12:05:55 +0100 + kallisto (0.46.1+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -35,6 +35,7 @@ Package: kallisto-examples Architecture: all Depends: ${misc:Depends} Recommends: kallisto +Multi-Arch: foreign Suggests: snakemake Description: near-optimal RNA-Seq quantification (example data) Kallisto is a program for quantifying abundances of transcripts from ===================================== debian/copyright ===================================== @@ -1,7 +1,8 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: kallisto Source: https://github.com/pachterlab/kallisto/releases -Files-Excluded: */htslib +Files-Excluded: ext/htslib + src/kseq.h Files: * Copyright: 2016-2017 Nicolas Bray, Harold Pimentel, Páll Melsted and Lior Pachter ===================================== debian/patches/htslib1.3 ===================================== @@ -0,0 +1,54 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Use kseq.h from htslib, not the bundled version +--- kallisto.orig/src/KmerIndex.cpp ++++ kallisto/src/KmerIndex.cpp +@@ -4,7 +4,7 @@ + #include <ctype.h> + #include <zlib.h> + #include <unordered_set> +-#include "kseq.h" ++#include <htslib/kseq.h> + + #ifndef KSEQ_INIT_READY + #define KSEQ_INIT_READY +--- kallisto.orig/src/ProcessReads.cpp ++++ kallisto/src/ProcessReads.cpp +@@ -1,6 +1,6 @@ + /* + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + #include <string> + #include <vector> + #include <unordered_map> +@@ -20,7 +20,7 @@ + #include <iomanip> + + #include "ProcessReads.h" +-#include "kseq.h" ++#include <htslib/kseq.h> + #include "PseudoBam.h" + #include "Fusion.hpp" + #include "BUSData.h" +--- kallisto.orig/src/ProcessReads.h ++++ kallisto/src/ProcessReads.h +@@ -2,7 +2,7 @@ + #define KALLISTO_PROCESSREADS_H + + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + #include <string> + #include <vector> + #include <unordered_map> +--- kallisto.orig/unit_tests/test_kmerhashtable.cpp ++++ kallisto/unit_tests/test_kmerhashtable.cpp +@@ -13,7 +13,7 @@ + #include "KmerHashTable.h" + + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + + #ifndef KSEQ_INIT_READY + #define KSEQ_INIT_READY ===================================== debian/patches/series ===================================== @@ -1 +1,3 @@ use_debian_packaged_htslib.patch +spelling +htslib1.3 ===================================== debian/patches/spelling ===================================== @@ -0,0 +1,13 @@ +From: Michael R. Crusoe +Subject: fix spelling typo +--- kallisto.orig/src/Inspect.h ++++ kallisto/src/Inspect.h +@@ -249,7 +249,7 @@ + const Contig& c = index.dbGraph.contigs[i]; + + if (c.seq.size() != c.length + k-1) { +- cerr << "Length and string dont match " << endl << "seq = " << c.seq << " (length = " << c.seq.size() << "), c.length = " << c.length << endl; ++ cerr << "Length and string don't match " << endl << "seq = " << c.seq << " (length = " << c.seq.size() << "), c.length = " << c.length << endl; + exit(1); + } + View it on GitLab: https://salsa.debian.org/med-team/kallisto/compare/79ce01c1e7c21ef09950fa0c79e02cac2c6abcca...7f4ecc0279abda0a6907f899d1b742fa913c24b4 -- View it on GitLab: https://salsa.debian.org/med-team/kallisto/compare/79ce01c1e7c21ef09950fa0c79e02cac2c6abcca...7f4ecc0279abda0a6907f899d1b742fa913c24b4 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
