[med-svn] [Git][med-team/kallisto][master] 4 commits: routine-update: Ready to upload to unstable

[Michael R. Crusoe]

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 <michael.crusoe at gmail.com>  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 <michael.crusoe at gmail.com>
+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
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