[med-svn] [adapterremoval] 04/07: New upstream version

[Andreas Tille]

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tille pushed a commit to branch master
in repository adapterremoval.

commit dc1ee7ae46155621f0df5d9a52a301eed43c4be2
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jul 17 12:59:19 2017 +0200

    New upstream version
---
 debian/changelog                        |  3 ++-
 debian/patches/add_missing_header.patch | 18 ------------------
 debian/patches/do_not_gunzip.patch      | 25 -------------------------
 debian/patches/series                   |  1 -
 4 files changed, 2 insertions(+), 45 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 185a1c5..49055c4 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,6 @@
-adapterremoval (2.2.1-2) UNRELEASED; urgency=medium
+adapterremoval (2.2.1a-1) UNRELEASED; urgency=medium
 
+  * New upstream version (adapt patches)
   * Enable letters in watch file expression
 
  -- Andreas Tille <tille at debian.org>  Mon, 17 Jul 2017 12:56:16 +0200
diff --git a/debian/patches/add_missing_header.patch b/debian/patches/add_missing_header.patch
deleted file mode 100644
index 34c8005..0000000
--- a/debian/patches/add_missing_header.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 22 Jun 2017 08:57:11 +0200
-Description: Deal with
-  src/fastq.cc: In member function 'ar::fastq::ntrimmed ar::fastq::trim_windowed_bases(bool, char, double)':
-  src/fastq.cc:198:24: error: 'accumulate' is not a member of 'std'
-       long running_sum = std::accumulate(m_qualities.begin(),
-                          ^~~
-
---- a/src/fastq.cc
-+++ b/src/fastq.cc
-@@ -24,6 +24,7 @@
- \*************************************************************************/
- #include <algorithm>
- #include <cmath>
-+#include <numeric>
- #include <stdexcept>
- #include <sstream>
- 
diff --git a/debian/patches/do_not_gunzip.patch b/debian/patches/do_not_gunzip.patch
deleted file mode 100644
index 03f8dae..0000000
--- a/debian/patches/do_not_gunzip.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 04 Dec 2016 17:31:19 +0100
-Description: No need to zip and unzip later
-
---- a/benchmark/benchmark.sh
-+++ b/benchmark/benchmark.sh
-@@ -308,14 +308,16 @@ function simulate_reads()
-                 mkdir -p "${DST}/"
- 
-                 # -c 0 = uncompressed output
--                if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c gzip -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
-+                if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c text -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
-                     > "${DST}/reads.stdout" 2> "${DST}/reads.stderr";
-                 then
-                     echo "Error simulated reads ..." > /dev/stderr
-                     exit 1
-                 fi
- 
--                gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz"
-+                if [ -e "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz" ] ; then
-+                    gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz"
-+                fi
-                 ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_1.fq" "${DST}_1.fq"
-                 ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_2.fq" "${DST}_2.fq"
-                 ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}.read.info" "${DST}.read.info"
diff --git a/debian/patches/series b/debian/patches/series
index c52bbfb..3af111a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
 adapt-benchmarking.patch
 reduce_benchmark_length.patch
 delete_adapterremoval1x_completely.patch
-add_missing_header.patch

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