debian/changelog

+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@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

 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

+From: Michael R. Crusoe <michael.crusoe@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

 use_debian_packaged_htslib.patch
+spelling
+htslib1.3

debian/patches/spelling

+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);
+       }
+