[med-svn] [fastx-toolkit] 03/03: add patch to explain -Q option

[Nadiya Sitdykova]

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rovenskasa-guest pushed a commit to branch master
in repository fastx-toolkit.

commit c9d74e76c7bb74ba89a5d299e5e0d19a1eb2ba2e
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Tue Jun 6 17:05:25 2017 -0400

    add patch to explain -Q option
---
 debian/changelog                            |  2 ++
 debian/patches/Q_option_documentation.patch | 54 +++++++++++++++++++++++++++++
 debian/patches/series                       |  1 +
 3 files changed, 57 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 9cbc0f3..af82771 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,8 @@ fastx-toolkit (0.0.14-4) unstable; urgency=low
   * Add tests for fastx_quality_stats and fastq_quality_filter
   * Fix typos in fastq_quality_filter test
   * Additional tests
+  * Add info about -Q option to help screens for commmands, where 
+    it's relevant
 
  -- Nadiya Sitdykova <rovenskasa at gmail.com>  Mon, 05 Jun 2017 17:55:44 -0400
 
diff --git a/debian/patches/Q_option_documentation.patch b/debian/patches/Q_option_documentation.patch
new file mode 100644
index 0000000..8f79cd7
--- /dev/null
+++ b/debian/patches/Q_option_documentation.patch
@@ -0,0 +1,54 @@
+Description: add information about -Q option to help screen for several commands
+Author: Nadiya Sitdykova rovenskasa at gmail.com
+Last-Update: 2017-06-06
+=============================================================================== 
+--- a/src/fastq_masker/fastq_masker.c
++++ b/src/fastq_masker/fastq_masker.c
+@@ -43,6 +43,7 @@ const char* usage=
+ "                  If [-o] is specified,  report will be printed to STDOUT.\n" \
+ "                  If [-o] is not specified (and output goes to STDOUT),\n" \
+ "                  report will be printed to STDERR.\n" \
++"   [-Q N]       = FASTQ ASCII offset. Default is 33.\n" \
+ "\n";
+ 
+ int min_quality_threshold=10;
+--- a/src/fastq_quality_converter/fastq_quality_converter.c
++++ b/src/fastq_quality_converter/fastq_quality_converter.c
+@@ -38,6 +38,7 @@ const char* usage=
+ "   [-z]         = Compress output with GZIP.\n" \
+ "   [-i INFILE]  = FASTA/Q input file. default is STDIN.\n" \
+ "   [-o OUTFILE] = FASTA output file. default is STDOUT.\n" \
++"   [-Q N]       = FASTQ ASCII offset. Default is 33.\n" \
+ "\n";
+ 
+ FASTX fastx;
+--- a/src/fastq_quality_filter/fastq_quality_filter.c
++++ b/src/fastq_quality_filter/fastq_quality_filter.c
+@@ -44,6 +44,7 @@ const char* usage=
+ "                  If [-o] is specified,  report will be printed to STDOUT.\n" \
+ "                  If [-o] is not specified (and output goes to STDOUT),\n" \
+ "                  report will be printed to STDERR.\n" \
++"   [-Q N]       = FASTQ ASCII offset. Default is 33.\n" \
+ "\n";
+ 
+ #define DO_NOT_TRIM_LAST_BASE (0)
+--- a/src/fastq_quality_trimmer/fastq_quality_trimmer.c
++++ b/src/fastq_quality_trimmer/fastq_quality_trimmer.c
+@@ -44,6 +44,7 @@ const char* usage=
+ "                  If [-o] is specified,  report will be printed to STDOUT.\n" \
+ "                  If [-o] is not specified (and output goes to STDOUT),\n" \
+ "                  report will be printed to STDERR.\n" \
++"   [-Q N]       = FASTQ ASCII offset. Default is 33.\n" \
+ "\n";
+ 
+ int min_quality_threshold=0;
+--- a/src/fastx_quality_stats/fastx_quality_stats.c
++++ b/src/fastx_quality_stats/fastx_quality_stats.c
+@@ -47,6 +47,7 @@ const char* usage=
+ "   [-i INFILE]  = FASTQ input file. default is STDIN.\n" \
+ "   [-o OUTFILE] = TEXT output file. default is STDOUT.\n" \
+ "   [-N]         = New output format (with more information per nucleotide/cycle).\n" \
++"   [-Q N]       = FASTQ ASCII offset. Default is 33.\n" \
+ "\n"\
+ "The *OLD* output TEXT file will have the following fields (one row per column):\n" \
+ "	column	= column number (1 to 36 for a 36-cycles read solexa file)\n" \
diff --git a/debian/patches/series b/debian/patches/series
index b2026fe..8ad229c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+Q_option_documentation.patch
 reproducible_build.patch

-- 
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