A new -b option to output abbreviated protein predictions.

For example, instead of

    BCSQ=splice_region|CD207|ENST00000410009|protein_coding,frameshift|\
    CD207|ENST00000410009|protein_coding|-|25EPPPKSGPSLVPGKTPTVRAALICLT\
    LVLVASVLLQAVLYPRFMGTISDVKTNVQLLKGRVDNISTLDSEIKKNSDGMEAAGVQIQMVNESLG\
    YVRSQFLKLKTSVEKANAQIQILTRSWEEVSTLNAQIPELKSDLEKASALNTKIRALQGSLENMSKL\
    LKRQNDILQVVSQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIY\
    WIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFI\
    CKRPYVPSEP*>25GASSQVRSISGPGENTHSPCCINLPDAGPGRLRPAAGRPLSPVYGHHIRCKDQ\
    CPVAERSCGQHQHPGF*|5507G>GC,

print

    BCSQ=splice_region|CD207|ENST00000410009|protein_coding,frameshift|\
    CD207|ENST00000410009|protein_coding|-|25E..329>25G..94|5507G>GC

Resolves samtools#957

csq.c

@@ -587,6 +587,7 @@ typedef struct _args_t
     int phase, quiet, local_csq;
     int ncsq_max, nfmt_bcsq;    // maximum number of csq per site that can be accessed from FORMAT/BCSQ
     int ncsq_small_warned;
+    int brief_predictions;
 
     int rid;                    // current chromosome
     tr_heap_t *active_tr;       // heap of active transcripts for quick flushing
@@ -2576,6 +2577,20 @@ void kput_vcsq(args_t *args, vcsq_t *csq, kstring_t *str)
         kputs(csq->vstr.s, str);
 }
 
+void kprint_aa_prediction(args_t *args, int beg, kstring_t *aa, kstring_t *str)
+{
+    if ( !args->brief_predictions )
+        kputs(aa->s, str);
+    else
+    {
+        int len = aa->l;
+        if ( aa->s[len-1]=='*' ) len--;
+        kputc(aa->s[0], str);
+        kputs("..", str);
+        kputw(beg+len, str);
+    }
+}
+
 void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, int iend, int dlen, int indel)
 {
     int i;
@@ -2684,12 +2699,12 @@ void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg,
     int aa_sbeg = tr->strand==STRAND_FWD ? node2sbeg(ibeg)/3+1 : (tlen - node2send(iend))/3+1;
     kputc_('|', &str);
     kputw(aa_rbeg, &str);
-    kputs(hap->tref.s, &str);
+    kprint_aa_prediction(args,aa_rbeg,&hap->tref,&str);
     if ( !(csq->type.type & CSQ_SYNONYMOUS_VARIANT) )
     {
         kputc_('>', &str);
         kputw(aa_sbeg, &str);
-        kputs(hap->tseq.s, &str);
+        kprint_aa_prediction(args,aa_sbeg,&hap->tseq,&str);
     }
     kputc_('|', &str);
 
@@ -3324,12 +3339,12 @@ int test_cds_local(args_t *args, bcf1_t *rec)
                     int aa_sbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (tr->nsref - 2*N_REF_PAD + node.dlen - node.sbeg - alen)/3+1;
                     kputc_('|', &str);
                     kputw(aa_rbeg, &str);
-                    kputs(tref->s, &str);
+                    kprint_aa_prediction(args,aa_rbeg,tref,&str);
                     if ( !(csq_type & CSQ_SYNONYMOUS_VARIANT) )
                     {
                         kputc_('>', &str);
                         kputw(aa_sbeg, &str);
-                        kputs(tseq->s, &str);
+                        kprint_aa_prediction(args,aa_sbeg,tseq,&str);
                     }
                     kputc_('|', &str);
                     kputw(rec->pos+1, &str);
@@ -3901,6 +3916,7 @@ static const char *usage(void)
         "   -g, --gff-annot <file>          gff3 annotation file\n"
         "\n"
         "CSQ options:\n"
+        "   -b, --brief-predictions         annotate with abbreviated protein-changing predictions\n"
         "   -c, --custom-tag <string>       use this tag instead of the default BCSQ\n"
         "   -l, --local-csq                 localized predictions, consider only one VCF record at a time\n"
         "   -n, --ncsq <int>                maximum number of consequences to consider per site [16]\n"
@@ -3947,6 +3963,7 @@ int main_csq(int argc, char *argv[])
         {"force",0,0,1},
         {"help",0,0,'h'},
         {"ncsq",1,0,'n'},
+        {"brief-predictions",0,0,'b'},
         {"custom-tag",1,0,'c'},
         {"local-csq",0,0,'l'},
         {"gff-annot",1,0,'g'},
@@ -3967,11 +3984,12 @@ int main_csq(int argc, char *argv[])
     };
     int c, targets_is_file = 0, regions_is_file = 0; 
     char *targets_list = NULL, *regions_list = NULL;
-    while ((c = getopt_long(argc, argv, "?hr:R:t:T:i:e:f:o:O:g:s:S:p:qc:ln:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "?hr:R:t:T:i:e:f:o:O:g:s:S:p:qc:ln:b",loptions,NULL)) >= 0)
     {
         switch (c) 
         {
             case  1 : args->force = 1; break;
+            case 'b': args->brief_predictions = 1; break;
             case 'l': args->local_csq = 1; break;
             case 'c': args->bcsq_tag = optarg; break;
             case 'q': args->quiet++; break;

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: 2019-04-05 09:10 BST
+.\"      Date: 2019-04-15 17:40 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2019\-04\-05 09:10 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2019\-04\-15 17:40 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\-04\-05 09:10 BST\fR and refers to bcftools git version \fB1\&.9\-129\-g6027d36+\fR\&.
+This manual page was last updated \fB2019\-04\-15 17:40 BST\fR and refers to bcftools git version \fB1\&.9\-141\-gbe4494b+\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\&.
@@ -1828,6 +1828,13 @@ Symbolic alleles are not supported\&. They will remain unannotated in the output
 use this custom tag to store consequences rather than the default BCSQ tag
 .RE
 .PP
+\fB\-b, \-\-brief\-predictions\fR
+.RS 4
+annotate with abbreviated protein\-changing predictions\&. That is, instead of writing the whole modified protein sequence with potentially hundreds of aminoacids, only an abbreviated version such as
+\fI25E\&.\&.329>25G\&.\&.94\fR
+will be written
+.RE
+.PP
 \fB\-e, \-\-exclude\fR \fIEXPRESSION\fR
 .RS 4
 exclude sites for which

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="idp25035840"></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="idp25163040"></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>2019-04-05 09:10 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.9-129-g6027d36+</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>2019-04-15 17:40 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.9-141-gbe4494b+</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
@@ -1043,6 +1043,12 @@
 </span></dt><dd>
     use this custom tag to store consequences rather than the default BCSQ tag
 </dd><dt><span class="term">
+<span class="strong"><strong>-b, --brief-predictions</strong></span>
+</span></dt><dd>
+    annotate with abbreviated protein-changing predictions. That is, instead of writing
+    the whole modified protein sequence with potentially hundreds of aminoacids, only an
+    abbreviated version such as <span class="emphasis"><em>25E..329&gt;25G..94</em></span> will be written
+</dd><dt><span class="term">
 <span class="strong"><strong>-e, --exclude</strong></span> <span class="emphasis"><em>EXPRESSION</em></span>
 </span></dt><dd>
     exclude sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see

doc/bcftools.txt

@@ -1083,6 +1083,11 @@ output VCF and are ignored for the prediction analysis.
 *-c, --custom-tag* 'STRING'::
     use this custom tag to store consequences rather than the default BCSQ tag
 
+*-b, --brief-predictions*::
+    annotate with abbreviated protein-changing predictions. That is, instead of writing
+    the whole modified protein sequence with potentially hundreds of aminoacids, only an
+    abbreviated version such as '25E..329>25G..94' will be written
+
 *-e, --exclude* 'EXPRESSION'::
     exclude sites for which 'EXPRESSION' is true. For valid expressions see
     *<<expressions,EXPRESSIONS>>*.

test/csq/ENST00000410009/frameshift.1.cmd

@@ -0,0 +1 @@
+{bin}/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | {bin}/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'

test/csq/ENST00000410009/frameshift.1.cmd.out

@@ -0,0 +1 @@
+5507	G	GC	frameshift|CD207|ENST00000410009|protein_coding|-|25E..329>25G..94|5507G>GC,splice_region|CD207|ENST00000410009|protein_coding

test/csq/ENST00000410009/frameshift.2.cmd

@@ -0,0 +1 @@
+{bin}/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | {bin}/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'

test/csq/ENST00000410009/frameshift.2.cmd.out

@@ -0,0 +1 @@
+5507	G	GC	frameshift|CD207|ENST00000410009|protein_coding|-|25E..329>25G..94|5507G>GC,splice_region|CD207|ENST00000410009|protein_coding