[med-svn] [adapterremoval] 02/04: Fix spelling
Andreas Tille
tille at debian.org
Sun Dec 4 16:45:40 UTC 2016
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tille pushed a commit to branch master
in repository adapterremoval.
commit 3611af101d566c95a6cba5732bb61aeb8639560f
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 4 17:32:39 2016 +0100
Fix spelling
---
debian/changelog | 4 ++
debian/patches/series | 1 +
debian/patches/spelling.patch | 102 ++++++++++++++++++++++++++++++++++++++++++
3 files changed, 107 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 6f31f77..1724a8a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,13 @@
adapterremoval (2.2.0-1) UNRELEASED; urgency=medium
+ [ Kevin Murray ]
* Team upload
* New upstream version 2.2.0 (Closes: #846664)
* Refresh patches
+ [ Andreas Tille ]
+ * Fix spelling
+
-- Kevin Murray <spam at kdmurray.id.au> Sun, 04 Dec 2016 17:22:09 +0100
adapterremoval (2.1.7-1) unstable; urgency=medium
diff --git a/debian/patches/series b/debian/patches/series
index 3af111a..44f71e6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
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
new file mode 100644
index 0000000..cd557a3
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,102 @@
+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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