Commit e439282c authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1.10.2

parent b6f8d993

Makefile

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@@ -103,7 +103,7 @@ endif 


include config.mk



PACKAGE_VERSION = 1.10

PACKAGE_VERSION = 1.10.2



# 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

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## Release 1.10.2 (19th December 2019)



This is a release fix that corrects minor inconsistencies discovered in

previous deliverables.





## Release 1.10 (6th December 2019)

doc/bcftools.1

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@@ -2,12 +2,12 @@ 
.\"     Title: bcftools

.\"    Author: [see the "AUTHORS" section]

.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>

.\"      Date: 2019-12-06

.\"      Date: 2019-12-19

.\"    Manual: \ \&

.\"    Source: \ \&

.\"  Language: English

.\"

.TH "BCFTOOLS" "1" "2019\-12\-06" "\ \&" "\ \&"

.TH "BCFTOOLS" "1" "2019\-12\-19" "\ \&" "\ \&"

.\" -----------------------------------------------------------------

.\" * 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\-12\-06\fR and refers to bcftools git version \fB1\&.10\fR\&.

This manual page was last updated \fB2019\-12\-19\fR and refers to bcftools git version \fB1\&.10\&.2\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\&.
@@ -3130,6 +3130,13 @@ reference sequence\&. Supplying this option will turn on left\-alignment and nor 
option below\&.

.RE

.PP

\fB\-\-force\fR

.RS 4

try to proceed with

\fB\-m\-\fR

even if malformed tags with incorrect number of fields are encountered, discarding such tags\&. (Experimental, use at your own risk\&.)

.RE

.PP

\fB\-m, \-\-multiallelics\fR \fB\-\fR|\fB+\fR[\fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIany\fR]

.RS 4

split multiallelic sites into biallelic records (\fB\-\fR) or join biallelic sites into multiallelic records (\fB+\fR)\&. An optional type string can follow which controls variant types which should be split or merged together: If only SNP records should be split or merged, specify

doc/bcftools.html

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<?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="idp212896"></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="idp25229120"></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
@@ -10,7 +10,7 @@ read simultaneously, they must be indexed and therefore also compressed. 
(Note that files with non-standard index names can be accessed as e.g.

"<code class="literal">bcftools view -r X:2928329 file.vcf.gz##idx##non-standard-index-name</code>".)</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>2019-12-06</strong></span> and refers to bcftools git version <span class="strong"><strong>1.10</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>2019-12-19</strong></span> and refers to bcftools git version <span class="strong"><strong>1.10.2</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
@@ -1895,6 +1895,11 @@ the <span class="strong"><strong><a class="link" href="#fasta_ref">--fasta-ref</ 
    and normalization, however, see also the <span class="strong"><strong><a class="link" href="#do_not_normalize">--do-not-normalize</a></strong></span>

    option below.

</dd><dt><span class="term">

<span class="strong"><strong>--force</strong></span>

</span></dt><dd>

    try to proceed with <span class="strong"><strong>-m-</strong></span> even if malformed tags with incorrect number of fields

    are encountered, discarding such tags. (Experimental, use at your own risk.)

</dd><dt><span class="term">

<span class="strong"><strong>-m, --multiallelics</strong></span> <span class="strong"><strong>-</strong></span>|<span class="strong"><strong>+</strong></span>[<span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>any</em></span>]

</span></dt><dd>

    split multiallelic sites into biallelic records (<span class="strong"><strong>-</strong></span>) or join

doc/bcftools.txt

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@@ -1924,6 +1924,10 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied. 
    and normalization, however, see also the *<<do_not_normalize,--do-not-normalize>>*

    option below.



*--force*::

    try to proceed with *-m-* even if malformed tags with incorrect number of fields

    are encountered, discarding such tags. (Experimental, use at your own risk.)



*-m, --multiallelics* *-*|*+*['snps'|'indels'|'both'|'any']::

    split multiallelic sites into biallelic records (*-*) or join

    biallelic sites into multiallelic records (*+*). An optional type string