Merge branch 'develop' of github.com:samtools/bcftools into develop

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

consensus.c

@@ -123,9 +123,17 @@ typedef struct
 }
 args_t;
 
+static void destroy_chain(chain_t *chain)
+{
+    if ( !chain ) return;
+    free(chain->ref_gaps);
+    free(chain->alt_gaps);
+    free(chain->block_lengths);
+    free(chain);
+}
 static chain_t* init_chain(chain_t *chain, int ref_ori_pos)
 {
-//     fprintf(stderr, "init_chain(*chain, ref_ori_pos=%d)\n", ref_ori_pos);
+    if ( chain ) destroy_chain(chain);
     chain = (chain_t*) calloc(1,sizeof(chain_t));
     chain->num = 0;
     chain->block_lengths = NULL;
@@ -137,18 +145,6 @@ static chain_t* init_chain(chain_t *chain, int ref_ori_pos)
     return chain;
 }
 
-static void destroy_chain(args_t *args)
-{
-    chain_t *chain = args->chain;
-    free(chain->ref_gaps);
-    free(chain->alt_gaps);
-    free(chain->block_lengths);
-    free(chain);
-    chain = NULL;
-    free(args->chr);
-    args->chr = NULL;
-}
-
 static void print_chain(args_t *args)
 {
     /*
@@ -197,7 +193,7 @@ static void print_chain(args_t *args)
 
 static void push_chain_gap(chain_t *chain, int ref_start, int ref_len, int alt_start, int alt_len)
 {
-//     fprintf(stderr, "push_chain_gap(*chain, ref_start=%d, ref_len=%d, alt_start=%d, alt_len=%d)\n", ref_start, ref_len, alt_start, alt_len);
+    // fprintf(stderr, "push_chain_gap(chain=%p, ref_start=%d, ref_len=%d, alt_start=%d, alt_len=%d)\n", chain, ref_start, ref_len, alt_start, alt_len);
     int num = chain->num;
 
     if (num && ref_start <= chain->ref_last_block_ori) {
@@ -305,6 +301,7 @@ static void destroy_data(args_t *args)
     if ( args->chain_fname )
         if ( fclose(args->fp_chain) ) error("Close failed: %s\n", args->chain_fname);
     if ( fclose(args->fp_out) ) error("Close failed: %s\n", args->output_fname);
+    destroy_chain(args->chain);
 }
 
 static void init_region(args_t *args, char *line)
@@ -346,12 +343,8 @@ static void init_region(args_t *args, char *line)
     bcf_sr_seek(args->files,line,args->fa_ori_pos);
     if ( tmp_ptr ) *tmp_ptr = tmp;
     fprintf(args->fp_out,">%s%s\n",args->chr_prefix?args->chr_prefix:"",line);
-    if (args->chain_fname )
-    {
+    if ( args->chain_fname )
         args->chain = init_chain(args->chain, args->fa_ori_pos);
-    } else {
-        args->chain = NULL;
-    }
 }
 
 static bcf1_t **next_vcf_line(args_t *args)
@@ -949,10 +942,8 @@ static void consensus(args_t *args)
         if ( str.s[0]=='>' )
         {
             // new sequence encountered
-            if (args->chain) {
-                print_chain(args);
-                destroy_chain(args);
-            }
+            if ( args->chain ) print_chain(args);
+
             // apply all cached variants and variants that might have been missed because of short fasta (see test/consensus.9.*)
             bcf1_t **rec_ptr = NULL;
             while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
@@ -1026,11 +1017,7 @@ static void consensus(args_t *args)
         if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) break;
         apply_variant(args, rec);
     }
-    if (args->chain)
-    {
-        print_chain(args);
-        destroy_chain(args);
-    }
+    if (args->chain) print_chain(args);
     if ( args->absent_allele ) apply_absent(args, HTS_POS_MAX);
     flush_fa_buffer(args, 0);
     bgzf_close(fasta);

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 ]