[med-svn] [bcftools] 07/10: Fix spelling errors

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository bcftools.

commit c32c01f35aac1dff365144d554b86e90fa592ed0
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Nov 9 23:19:02 2015 -0800

    Fix spelling errors
---
 debian/patches/series         |  1 +
 debian/patches/spelling.patch | 53 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 9031066..14aee1b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ external-libs.patch
 compiler-flags.patch
 destdir.patch
 tests-pluginpath.patch
+spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..538a3f9
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,53 @@
+Description: Fix spelling errors
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-11-09
+--- bcftools.orig/doc/bcftools.1
++++ bcftools/doc/bcftools.1
+@@ -465,7 +465,7 @@
+ .\}
+ .SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
+ .sp
+-This command allows to add or remove annotations\&.
++This command allows one to add or remove annotations\&.
+ .PP
+ \fB\-a, \-\-annotations\fR \fIfile\fR
+ .RS 4
+@@ -779,7 +779,7 @@
+ likelihood of novel mutation for constrained
+ \fB\-C\fR
+ \fItrio\fR
+-calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explictly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as P [...]
++calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as  [...]
+ .RE
+ .PP
+ \fB\-p, \-\-pval\-threshold\fR \fIfloat\fR
+@@ -2123,7 +2123,7 @@
+ // Longer description used by \*(Aqbcftools +name \-h\*(Aq
+ const char *usage(void);
+ 
+-// Called once at startup, allows to initialize local variables\&.
++// Called once at startup, allows one to initialize local variables\&.
+ // Return 1 to suppress normal VCF/BCF header output, \-1 on critical
+ // errors, 0 otherwise\&.
+ int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);
+--- bcftools.orig/vcfcall.c
++++ bcftools/vcfcall.c
+@@ -169,7 +169,7 @@
+         sam = add_sample(sam, &n, &max, col_ends[0]+1, ploidy, &j);
+         if ( strcmp(col_ends[1]+1,"0") )    // father
+         {
+-            if ( fam->sample[CHILD]>=0 ) error("Multiple childs in %s [%s,%s]\n", str.s, sam[j],sam[fam->sample[CHILD]]);
++            if ( fam->sample[CHILD]>=0 ) error("Multiple children in %s [%s,%s]\n", str.s, sam[j],sam[fam->sample[CHILD]]);
+             fam->sample[CHILD] = j;
+             if ( fam->sample[FATHER]>=0 ) error("Two fathers in %s?\n", str.s);
+             sam = add_sample(sam, &n, &max, col_ends[1]+1, call->flag & (CALL_CHR_X|CALL_CHR_Y) ? 1 : 2, &fam->sample[FATHER]);
+@@ -189,7 +189,7 @@
+     }
+     assert( n==_n );
+     for (i=0; i<call->nfams; i++)
+-        assert( call->fams[i].sample[0]>=0 && call->fams[i].sample[1]>=0 && call->fams[i].sample[2]>=0 ); // multiple childs, not a trio
++        assert( call->fams[i].sample[0]>=0 && call->fams[i].sample[1]>=0 && call->fams[i].sample[2]>=0 ); // multiple children, not a trio
+ 
+     return sam;
+ }

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