This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository vcftools.
commit 313249c3ff101118300b37086baeb99e71fe16b3 Author: Andreas Tille <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/vcftools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
