[med-svn] [vcftools] 03/08: Fix spelling

[Andreas Tille]

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tille pushed a commit to branch master
in repository vcftools.

commit 313249c3ff101118300b37086baeb99e71fe16b3
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jul 3 22:08:08 2016 +0200

    Fix spelling
---
 debian/mans/fill-fs.1         |  2 +-
 debian/mans/vcftools.1        |  2 +-
 debian/patches/series         |  1 +
 debian/patches/spelling.patch | 42 ++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 45 insertions(+), 2 deletions(-)

diff --git a/debian/mans/fill-fs.1 b/debian/mans/fill-fs.1
index 22f708d..70f03dc 100644
--- a/debian/mans/fill-fs.1
+++ b/debian/mans/fill-fs.1
@@ -19,7 +19,7 @@ Do self\-masking of clustered variants within this range.
 Flanking sequence length [100]
 .TP
 \fB\-m\fR, \fB\-\-mask\-char\fR <char|lc>
-The character to use or "lc" for lowercase. This option must preceed
+The character to use or "lc" for lowercase. This option must precede
 \fB\-b\fR, \fB\-v\fR or \fB\-c\fR in order to take effect. With multiple files works
 .IP
 as a switch on the command line, see the example below [N]
diff --git a/debian/mans/vcftools.1 b/debian/mans/vcftools.1
index f6cb8f2..84bcae8 100644
--- a/debian/mans/vcftools.1
+++ b/debian/mans/vcftools.1
@@ -398,7 +398,7 @@ used to retain all INFO fields.
 .TP
 \fB\-\-extract\-FORMAT\-info\fR <string>
 Extract information from the genotype fields in the VCF file relating to a 
-specfied FORMAT identifier. For example, using the 
+specified FORMAT identifier. For example, using the
 option '\-\-extract\-FORMAT\-info GT' would extract the all of the GT 
 (i.e. Genotype) 
 entries. The resulting output file has the suffix '.<FORMAT_ID>.FORMAT'.
diff --git a/debian/patches/series b/debian/patches/series
index b296b73..ab12ab9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 temporary_test_fix.patch
+spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..017f03e
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,42 @@
+--- a/src/cpp/variant_file_output.cpp
++++ b/src/cpp/variant_file_output.cpp
+@@ -1016,7 +1016,7 @@ void variant_file::calc_r2_em(entry *e,
+ 		e2->parse_genotype_entry(ui, true);
+ 		e2->get_indv_GENOTYPE_ids(ui, geno2);
+ 		// TODO... not yet implemented...!
+-		LOG.error("Not yet implmented!\n");
++		LOG.error("Not yet implemented!\n");
+ 	}
+ }
+ 
+--- a/src/perl/fill-fs
++++ b/src/perl/fill-fs
+@@ -27,7 +27,7 @@ sub error
+         "   -b, --bed-mask <file>           Regions to mask (tabix indexed), multiple files can be given\n",
+         "   -c, --cluster <int>             Do self-masking of clustered variants within this range.\n",
+         "   -l, --length <int>              Flanking sequence length [100]\n",
+-        "   -m, --mask-char <char|lc>       The character to use or \"lc\" for lowercase. This option must preceed\n",
++        "   -m, --mask-char <char|lc>       The character to use or \"lc\" for lowercase. This option must precede\n",
+         "                                       -b, -v or -c in order to take effect. With multiple files works\n",
+         "                                        as a switch on the command line, see the example below [N]\n",
+         "   -r, --refseq <file>             The reference sequence.\n",
+@@ -59,7 +59,7 @@ sub parse_params
+     }
+     if ( !($$opts{length}=~/^\d+$/) ) { error("Expected integer after -l, got $$opts{length}\n"); }
+     if ( !exists($$opts{refseq}) ) { error("Missing the -r option.\n"); }
+-    if ( $mask_changed ) { error("The -m parameter must preceed -b, -v, or the file in order to take effect.\n"); }
++    if ( $mask_changed ) { error("The -m parameter must precede -b, -v, or the file in order to take effect.\n"); }
+     return $opts;
+ }
+ 
+--- a/src/cpp/vcftools.1
++++ b/src/cpp/vcftools.1
+@@ -640,7 +640,7 @@ This option is use to report mendel erro
+ .B --extract-FORMAT-info 
+ .I <string>
+ .RS 2
+-Extract information from the genotype fields in the VCF file relating to a specfied FORMAT identifier. The resulting output file has the suffix ".<FORMAT_ID>.FORMAT". For example, the following command would extract the all of the GT (i.e. Genotype) entries:
++Extract information from the genotype fields in the VCF file relating to a specified FORMAT identifier. The resulting output file has the suffix ".<FORMAT_ID>.FORMAT". For example, the following command would extract the all of the GT (i.e. Genotype) entries:
+ .br
+ .RS 2
+ .B vcftools

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