Merge version number bump and NEWS file from master

Makefile

@@ -104,7 +104,7 @@ endif
 
 include config.mk
 
-PACKAGE_VERSION = 1.15
+PACKAGE_VERSION = 1.15.1
 
 # If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
 # description of the working tree: either a release tag with the same value

NEWS

@@ -1,14 +1,24 @@
 ## Release a.b
 
+
 * New plugin `bcftools +variant-distance` to annotate records with distance to the
   nearest variant (#1690)
 
+
+## Release 1.15.1 (7th April 2022)
+
+
 * bcftools annotate
 
     - New `-H, --header-line` convenience option to pass a header line on command line,
       this complements the existing `-h, --header-lines` option which requires a file
       with header lines
 
+* bcftools csq
+
+    - A list of consequence types supported by `bcftools csq` has been added to
+      the manual page. (#1671)
+
 * bcftools +fill-tags
 
     - Extend generalized functions so that FORMAT tags can be filled as well, for example:
@@ -20,6 +30,11 @@
 
 * bcftools norm
 
+    - Fix an assertion failure triggered when a faulty VCF file with a '-'
+      character in the REF allele was used with `bcftools norm --atomize`.  This
+      option now checks that the REF allele only includes the allowed characters
+      A, C, G, T and N. (#1668)
+
     - Fix the loss of phasing in half-missing genotypes in variant atomization (#1689)
 
 * bcftools roh

doc/bcftools.1

@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHOR(S)" section]
 .\" Generator: Asciidoctor 2.0.16.dev
-.\"      Date: 2022-02-21
+.\"      Date: 2022-04-07
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2022-02-21" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2022-04-07" "\ \&" "\ \&"
 .ie \n(.g .ds Aq \(aq
 .el       .ds Aq '
 .ss \n[.ss] 0
@@ -51,7 +51,7 @@ 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 \fB2022\-02\-21\fP and refers to bcftools git version \fB1.15\fP.
+This manual page was last updated \fB2022\-04\-07\fP and refers to bcftools git version \fB1.15.1\fP.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0.1.19 is \fBnot\fP
@@ -2177,6 +2177,39 @@ see \fBCommon Options\fP
 .fam
 .fi
 .if n .RE
+.sp
+\fBSupported consequence types\fP
+.sp
+.if n .RS 4
+.nf
+.fam C
+3_prime_utr
+5_prime_utr
+coding_sequence
+feature_elongation
+frameshift
+inframe_altering
+inframe_deletion
+inframe_insertion
+intergenic
+intron
+missense
+non_coding
+splice_acceptor
+splice_donor
+splice_region
+start_lost
+start_retained
+stop_gained
+stop_lost
+stop_retained
+synonymous
+.fam
+.fi
+.if n .RE
+.sp
+See also \c
+.URL "https://ensembl.org/info/genome/variation/prediction/predicted_data.html" "" ""
 .SS "bcftools filter \fI[OPTIONS]\fP \fIFILE\fP"
 .sp
 Apply fixed\-threshold filters.

doc/bcftools.html

@@ -50,7 +50,7 @@ <h2 id="_description">DESCRIPTION</h2>
 <div class="sect2">
 <h3 id="_version">VERSION</h3>
 <div class="paragraph">
-<p>This manual page was last updated <strong>2022-02-21</strong> and refers to bcftools git version <strong>1.15</strong>.</p>
+<p>This manual page was last updated <strong>2022-04-07</strong> and refers to bcftools git version <strong>1.15.1</strong>.</p>
 </div>
 </div>
 <div class="sect2">
@@ -1911,6 +1911,37 @@ <h3 id="csq">bcftools csq <em>[OPTIONS]</em> <em>FILE</em></h3>
     BCSQ=*missense|PER3|ENST00000361923|+|1028M&gt;1028T|7890117T&gt;C</pre>
 </div>
 </div>
+<div class="paragraph">
+<p><strong>Supported consequence types</strong></p>
+</div>
+<div class="listingblock">
+<div class="content">
+<pre>3_prime_utr
+5_prime_utr
+coding_sequence
+feature_elongation
+frameshift
+inframe_altering
+inframe_deletion
+inframe_insertion
+intergenic
+intron
+missense
+non_coding
+splice_acceptor
+splice_donor
+splice_region
+start_lost
+start_retained
+stop_gained
+stop_lost
+stop_retained
+synonymous</pre>
+</div>
+</div>
+<div class="paragraph">
+<p>See also <a href="https://ensembl.org/info/genome/variation/prediction/predicted_data.html" class="bare">https://ensembl.org/info/genome/variation/prediction/predicted_data.html</a></p>
+</div>
 </div>
 <div class="sect2">
 <h3 id="filter">bcftools filter <em>[OPTIONS]</em> <em>FILE</em></h3>
@@ -4988,7 +5019,7 @@ <h2 id="_copying">COPYING</h2>
 </div>
 <div id="footer">
 <div id="footer-text">
-Last updated 2022-02-21 11:43:27 UTC
+Last updated 2022-04-07 16:32:56 +0100
 </div>
 </div>
 </body>

version.sh

@@ -24,7 +24,7 @@
 # DEALINGS IN THE SOFTWARE.
 
 # Master version, for use in tarballs or non-git source copies
-VERSION=1.15
+VERSION=1.15.1
 
 # If we have a git clone, then check against the current tag
 if [ -e .git ]