[med-svn] [adapterremoval] 03/05: debhelper 10
Andreas Tille
tille at debian.org
Thu Jun 22 07:15:07 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository adapterremoval.
commit ad3046984147528b0e3f06ad995ddd2084cd14d3
Author: Andreas Tille <tille at debian.org>
Date: Thu Jun 22 08:54:40 2017 +0200
debhelper 10
---
debian/changelog | 8 ++++
debian/compat | 2 +-
debian/control | 2 +-
debian/patches/series | 1 -
debian/patches/spelling.patch | 102 ------------------------------------------
5 files changed, 10 insertions(+), 105 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 53e4410..5ff79c2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+adapterremoval (2.2.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Drop spelling patch
+ * debhelper 10
+
+ -- Andreas Tille <tille at debian.org> Thu, 22 Jun 2017 08:52:57 +0200
+
adapterremoval (2.2.0-1) unstable; urgency=medium
[ Kevin Murray ]
diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index 5f7f0bf..1ede848 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
zlib1g-dev,
libbz2-dev,
libgtest-dev,
diff --git a/debian/patches/series b/debian/patches/series
index 44f71e6..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
-spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index cd557a3..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,102 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 04 Dec 2016 17:31:19 +0100
-Description: Fix spelling
-
---- a/AdapterRemoval.pod
-+++ b/AdapterRemoval.pod
-@@ -11,7 +11,7 @@ B<AdapterRemoval> --file1 filename [--fi
-
- =head1 DESCRIPTION
-
--B<AdapterRemoval> reads either one FASTQ file (single ended mode) or two FASTQ files (paired ended mode). It removes the residual adapter sequence from the reads and optionally trims Ns from the reads, and low qualities bases using the quality string, and collapses overlapping paired ended mates into one read. Reads are discarded if the remaining genomic part is too short, or if the read contains more than an (user specified) amount of amigious nucleotides ('N'). These operations may be [...]
-+B<AdapterRemoval> reads either one FASTQ file (single ended mode) or two FASTQ files (paired ended mode). It removes the residual adapter sequence from the reads and optionally trims Ns from the reads, and low qualities bases using the quality string, and collapses overlapping paired ended mates into one read. Reads are discarded if the remaining genomic part is too short, or if the read contains more than an (user specified) amount of amigious nucleotides ('N'). These operations may be [...]
-
- Alternatively, B<AdapterRemoval> may attempt to reconstruct a consensus adapter sequences from paired-ended data, in order to allow the identification of the adapter sequences originally used, and thereby ensure proper trimming of these reads.
-
-@@ -42,11 +42,11 @@ If set, input is expected to be a single
-
- =item B<--interleaved-ouput>
-
--If set, and AdapterRemoval is processing paired-end reads, retained pairs of reads are written to a single FASTQ file, one pair after each otehr (read1/1, read1/2, read2/1, read2/2, etc.). By default, this file is named I<basename.paired.truncated>, but this may be changed using the I<--output1> option.
-+If set, and AdapterRemoval is processing paired-end reads, retained pairs of reads are written to a single FASTQ file, one pair after each other (read1/1, read1/2, read2/1, read2/2, etc.). By default, this file is named I<basename.paired.truncated>, but this may be changed using the I<--output1> option.
-
- =item B<--combined-output>
-
--If set, all reads are written to the same file(s), specified by --output1 and --output2. Each read is futher marked by either a "PASSED" or a "FAILED" flag, and any read that has been FAILED (including the mate for collapsed reads) are replaced with a single 'N' with Phred score 0. This option can be combined with --interleaved / --interleaved-output to write all reads to a single output file specified with --output1.
-+If set, all reads are written to the same file(s), specified by --output1 and --output2. Each read is further marked by either a "PASSED" or a "FAILED" flag, and any read that has been FAILED (including the mate for collapsed reads) are replaced with a single 'N' with Phred score 0. This option can be combined with --interleaved / --interleaved-output to write all reads to a single output file specified with --output1.
-
- =item B<--basename> I<filename>
-
-@@ -318,7 +318,7 @@ Note that in the case of paired-end adap
-
- If we did not know the adapter sequences for paired-end reads, AdapterRemoval may be used to generate a consensus adapter sequence based on fragments identified as belonging to the adapters through pairwise alignments of the reads, provided that the data set contains only a single adpater sequence (not counting differences in index sequences).
-
--In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not nessesary to specify this tail when using the I<--adapter1> or I<--adapter2> command-line options. The characters shown under each of the consensus sequences represented the phred-encoded fraction of bases identical to the consensus base, with adapter 1 containing the index CACCTA:
-+In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not necessary to specify this tail when using the I<--adapter1> or I<--adapter2> command-line options. The characters shown under each of the consensus sequences represented the phred-encoded fraction of bases identical to the consensus base, with adapter 1 containing the index CACCTA:
-
- $ AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq
-
---- a/src/adapterset.cc
-+++ b/src/adapterset.cc
-@@ -213,7 +213,7 @@ bool check_barcodes_sequences(const fast
- std::stringstream error;
- error << "Duplicate mate 1 barcodes found in '"
- << filename << "': "<< prev->first << ". Even if these "
-- "are assosiated with different mate 2 barcodes, it "
-+ "are associated with different mate 2 barcodes, it "
- "is not possible to distinguish between these in "
- "single-end mode!";
-
---- a/src/fastq.cc
-+++ b/src/fastq.cc
-@@ -334,7 +334,7 @@ void fastq::validate_paired_reads(fastq&
- if (info1.mate == mate_info::unknown || info2.mate == mate_info::unknown) {
- error << "\n\nNote that AdapterRemoval by determines the mate "
- "numbers as the digit found at the end of the read name, "
-- "if this is preceeded by the character '"
-+ "if this is preceded by the character '"
- << mate_separator
- << "'; if these data makes use of a different character to "
- "separate the mate number from the read name, then you "
---- a/src/main_adapter_id.cc
-+++ b/src/main_adapter_id.cc
-@@ -360,7 +360,7 @@ public:
- chunk_vec process(analytical_chunk* chunk)
- {
- if (!chunk) {
-- throw std::invalid_argument("sink recieved NULL chunk");
-+ throw std::invalid_argument("sink received NULL chunk");
- }
-
- const fastq empty_adapter("dummy", "", "");
---- a/src/main_adapter_rm.cc
-+++ b/src/main_adapter_rm.cc
-@@ -135,7 +135,7 @@ void write_settings(const userconfig& co
- << "\nQuality score max (input): " << config.quality_input_fmt->max_score()
- << "\nQuality format (output): " << config.quality_output_fmt->name()
- << "\nQuality score max (output): " << config.quality_output_fmt->max_score()
-- << "\nMate-number seperator (input): '" << config.mate_separator << "'"
-+ << "\nMate-number separator (input): '" << config.mate_separator << "'"
- << "\nTrimming Ns: " << ((config.trim_ambiguous_bases) ? "Yes" : "No")
- << "\nTrimming Phred scores <= " << config.low_quality_score
- << ": " << (config.trim_by_quality ? "Yes" : "No")
---- a/src/userconfig.cc
-+++ b/src/userconfig.cc
-@@ -171,7 +171,7 @@ userconfig::userconfig(const std::string
- new argparse::flag(&combined_output,
- "If set, all reads are written to the same file(s), specified by "
- "--output1 and --output2 (--output1 only if --interleaved-output "
-- "is not set). Each read is futher marked by either a \"PASSED\" "
-+ "is not set). Each read is further marked by either a \"PASSED\" "
- "or a \"FAILED\" flag, and any read that has been FAILED "
- "(including the mate for collapsed reads) are replaced with a "
- "single 'N' with Phred score 0 [current: %default].");
-@@ -320,7 +320,7 @@ userconfig::userconfig(const std::string
- new argparse::knob(&min_adapter_overlap, "LENGTH",
- "In single-end mode, reads are only trimmed if the overlap "
- "between read and the adapter is at least X bases long, not "
-- "counting ambiguous nucleotides (N); this is independant of the "
-+ "counting ambiguous nucleotides (N); this is independent of the "
- "--minalignmentlength when using --collapse, allowing a "
- "conservative selection of putative complete inserts while "
- "ensuring that all possible adapter contamination is trimmed "
--
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