Keep compiler happy, get rid of the harmless "igrp may be used uninit…

…ialized" warning
overerd · May 8, 2019 · 367492e · 367492e
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diff --git a/doc/bcftools.1 b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2019-05-03 14:49 BST
+.\"      Date: 2019-05-06 15:45 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2019\-05\-03 14:49 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2019\-05\-06 15:45 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2019\-05\-03 14:49 BST\fR and refers to bcftools git version \fB1\&.9\-154\-g4c250d8+\fR\&.
+This manual page was last updated \fB2019\-05\-06 15:45 BST\fR and refers to bcftools git version \fB1\&.9\-162\-g33ecfe8+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -988,6 +988,21 @@ take advantage of prior knowledge of population allele frequencies\&. The workfl
 .RE
 .\}
 .PP
+\fB\-G, \-\-group\-samples\fR \fIFILE\fR|\fI\-\fR
+.RS 4
+by default, all samples are assumed to come from a single population\&. This option allows to group samples into populations and apply the HWE assumption within but not across the populations\&.
+\fIFILE\fR
+is a tab\-delimited text file with sample names in the first column and group names in the second column\&. If
+\fI\-\fR
+is given instead, no HWE assumption is made at all and single\-sample calling is performed\&. (Note that in low coverage data this inflates the rate of false positives\&.) The
+\fB\-G\fR
+option requires the presence of FORMAT/AD generated at the
+\fBbcftools mpileup\fR
+step by providing the
+\fB\-a FMT/AD\fR
+option\&.
+.RE
+.PP
 \fB\-g, \-\-gvcf\fR \fIINT\fR
 .RS 4
 output also gVCF blocks of homozygous REF calls\&. The parameter

diff --git a/doc/bcftools.html b/doc/bcftools.html
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25138128"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp144448"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
 work in most, but not all situations. In general, whenever multiple VCFs are
 read simultaneously, they must be indexed and therefore also compressed.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2019-05-03 14:49 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.9-154-g4c250d8+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2019-05-06 15:45 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.9-162-g33ecfe8+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -495,6 +495,15 @@
 
     # Now before calling, stream the raw mpileup output through `bcftools annotate` to add the frequencies
     bcftools mpileup [...] -Ou | bcftools annotate -a AFs.tab.gz -h AFs.hdr -c CHROM,POS,REF,ALT,REF_AN,REF_AC -Ou | bcftools call -mv -F REF_AN,REF_AC [...]</pre><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-G, --group-samples</strong></span> <span class="emphasis"><em>FILE</em></span>|<span class="emphasis"><em>-</em></span>
+</span></dt><dd>
+    by default, all samples are assumed to come from a single population. This option allows to group samples
+    into populations and apply the HWE assumption within but not across the populations. <span class="emphasis"><em>FILE</em></span> is a tab-delimited
+    text file with sample names in the first column and group names in the second column. If <span class="emphasis"><em>-</em></span> is
+    given instead, no HWE assumption is made at all and single-sample calling is performed. (Note that
+    in low coverage data this inflates the rate of false positives.) The <span class="strong"><strong>-G</strong></span> option requires the presence of
+    FORMAT/AD generated at the <span class="strong"><strong>bcftools mpileup</strong></span> step by providing the <span class="strong"><strong>-a FMT/AD</strong></span> option.
+</dd><dt><span class="term">
 <span class="strong"><strong>-g, --gvcf</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     output also gVCF blocks of homozygous REF calls. The parameter <span class="emphasis"><em>INT</em></span> is the

diff --git a/mcall.c b/mcall.c
@@ -287,8 +287,10 @@ static void init_sample_groups(call_t *call)
                 grps->ngrp++;
             }
             int igrp;
-            if ( khash_str2int_get(grp2idx, ptr+1, &igrp)!=0 ) error("This should not happen, fixme: %s\n",ptr+1);
-            smpl2grp1[ismpl] = igrp+1;
+            if ( khash_str2int_get(grp2idx, ptr+1, &igrp)==0 )
+                smpl2grp1[ismpl] = igrp+1;
+            else
+                error("This should not happen, fixme: %s\n",ptr+1);
         }
         khash_str2int_destroy(grp2idx);