From e575c34406c37e8eafb365f20aec6f1d8a854b95 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Sat, 4 Aug 2018 13:51:26 +0000 Subject: [PATCH 01/12] Move qctool version to 2.0.1 --- bitbucket-pipelines.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index 21f2ebeff..b14dd0a77 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -3,9 +3,9 @@ pipelines: default: - step: script: - - wget http://www.well.ox.ac.uk/~gav/resources/qctool_v2.0-rc9-Ubuntu14.04-x86_64.tgz - - tar -xzf qctool_v2.0-rc9-Ubuntu14.04-x86_64.tgz - - cp qctool_v2.0-rc9-Ubuntu14.04-x86_64/qctool /usr/bin/ + - wget http://www.well.ox.ac.uk/~gav/resources/qctool_v2.0.1-Ubuntu14.04-x86_64.tgz + - tar -xzf qctool_v2.0.1-Ubuntu14.04-x86_64.tgz + - cp qctool_v2.0.1-Ubuntu14.04-x86_64/qctool /usr/bin/ - qctool - apt-get install --assume-yes zlib1g-dev - apt-get install --assume-yes python-pip From 0bfb260ef8c070bad462a14b9be99b0baadbcaf3 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Tue, 7 Aug 2018 09:00:44 +0000 Subject: [PATCH 02/12] bitbucket-pipelines: use my 14.04 build docker image --- bitbucket-pipelines.yml | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index b14dd0a77..f2d75af59 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -1,20 +1,11 @@ -image: atlassian/default-image:latest +image: gavinband/ubuntu-14.04-build pipelines: default: - step: script: - - wget http://www.well.ox.ac.uk/~gav/resources/qctool_v2.0.1-Ubuntu14.04-x86_64.tgz - - tar -xzf qctool_v2.0.1-Ubuntu14.04-x86_64.tgz - - cp qctool_v2.0.1-Ubuntu14.04-x86_64/qctool /usr/bin/ - - qctool - - apt-get install --assume-yes zlib1g-dev - - apt-get install --assume-yes python-pip - - python -m pip install robotframework - - qctool -g example/example.16bits.bgen -og /tmp/x.vcf - ./waf configure - ./waf - cd test/functional - - mkdir -p test-reports/-o - + - mkdir -p test-reports/ - pybot -o output.xml -l log.html -r report.html -d test-reports -x xunit.xml ./tests.txt From e3c0a416cf90a766fec708c9e73e91d9d7e71a22 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Tue, 7 Aug 2018 09:01:55 +0000 Subject: [PATCH 03/12] Pull rbgen test changes from master --- test/functional/test_rbgen.sh | 38 +++++++++++++++++++++++++++++++++++ test/functional/tests.txt | 4 ++++ 2 files changed, 42 insertions(+) create mode 100755 test/functional/test_rbgen.sh diff --git a/test/functional/test_rbgen.sh b/test/functional/test_rbgen.sh new file mode 100755 index 000000000..3b3d42c81 --- /dev/null +++ b/test/functional/test_rbgen.sh @@ -0,0 +1,38 @@ +#!/bin/bash +R="$1" +RBGEN="${2}" +if [[ ${R} == '' ]]; then + R='R' +fi +if [[ ${RBGEN} == '' ]]; then + RBGEN=build/R/rbgen +fi + +${R} CMD INSTALL ${RBGEN} +${R} --vanilla << HERE_DOC +library( rbgen ) + +## Test we can load data +D = bgen.load( "example/example.16bits.bgen", ranges = data.frame( chromosome = '01', start = 0, end = 100000 )) +str( D ) +head( D\$variants ) +D\$data[1,1:10,1:3] + +## Test we can load data on a subset of samples +samples = c( "sample_001", "sample_102", "sample_050", "sample_499" ) +E = bgen.load( "example/example.16bits.bgen", ranges = data.frame( chromosome = '01', start = 0, end = 100000 ), samples = samples ) +stopifnot( length( which( E\$data != D\$data[,samples,] ) ) == 0 ) +stopifnot( length( which( D\$variants != E\$variants )) == 0 ) + +## Test we can load data for some specific rsid +rsids = c( "RSID_10", "RSID_20", "RSID_171", "RSID_9" ) +F = bgen.load( "example/example.16bits.bgen", rsids = rsids ) +str( F ) +head( F\$variants ) +F\$data + +## Check we can load complex data +D = bgen.load( "example/complex.bgen", data.frame( chromosome = '01', start = 0, end = 1000000 ), max_entries_per_sample = 50 ) +str(D) + +HERE_DOC diff --git a/test/functional/tests.txt b/test/functional/tests.txt index fe7a7944c..e3fe061ca 100644 --- a/test/functional/tests.txt +++ b/test/functional/tests.txt @@ -4,6 +4,7 @@ ${HOME} %{HOME} ${BUILDDIR} ${BASEDIR}/build ${TMPDIR} ${BUILDDIR}/test/functional/tmp ${BGENIX} ${BUILDDIR}/apps/bgenix +${RBGEN} ${BUILDDIR}/R/rbgen ${QCTOOL} qctool ${UNITTEST} ${BUILDDIR}/test/unit/test_bgen @@ -39,6 +40,9 @@ Bgenix lists variants ${length}= Get length ${lines} Should be equal as integers ${length} 202 +Rbgen loads data + Run process ./test_rbgen.sh R ${RBGEN} + *** Keywords *** Create empty temp directory From 121dfc90e182f94a2b539732c62046dd12046f17 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Fri, 25 Jan 2019 09:07:22 +0000 Subject: [PATCH 04/12] update docs --- doc/html/bgen_format.html | 1 - doc/html/bgen_format_v1.0.html | 106 ------ doc/html/index.html | 99 +++++- doc/html/spec/latest.html | 1 + .../{bgen_format_v1.1.html => spec/v1.1.html} | 89 +----- .../{bgen_format_v1.2.html => spec/v1.2.html} | 284 +--------------- .../{bgen_format_v1.3.html => spec/v1.3.html} | 302 +----------------- doc/html/style.css | 31 +- 8 files changed, 151 insertions(+), 762 deletions(-) delete mode 120000 doc/html/bgen_format.html delete mode 100644 doc/html/bgen_format_v1.0.html mode change 120000 => 100644 doc/html/index.html create mode 120000 doc/html/spec/latest.html rename doc/html/{bgen_format_v1.1.html => spec/v1.1.html} (65%) rename doc/html/{bgen_format_v1.2.html => spec/v1.2.html} (63%) rename doc/html/{bgen_format_v1.3.html => spec/v1.3.html} (62%) diff --git a/doc/html/bgen_format.html b/doc/html/bgen_format.html deleted file mode 120000 index 0735d0d78..000000000 --- a/doc/html/bgen_format.html +++ /dev/null @@ -1 +0,0 @@ -bgen_format_v1.3.html \ No newline at end of file diff --git a/doc/html/bgen_format_v1.0.html b/doc/html/bgen_format_v1.0.html deleted file mode 100644 index 18b4bcc5b..000000000 --- a/doc/html/bgen_format_v1.0.html +++ /dev/null @@ -1,106 +0,0 @@ - - - - - - -
-
- The BGEN format -
- -
- A compressed binary format for typed and imputed genotype data -
-
-

- This page documents v1.0 of the BGEN format, which is now deprecated. - This format should not be used for new files. See here for the most recent - version of the BGEN format. -

-

Note: The data layout documented here has the limitation that alleles can be only 1 character long. - This prevents its use with (for example) the latest 1000 genomes data release, which contains structural variants many kilobases long. - Version 1.1 was developed to be backwards-compatible with this format, and addresses this issue. -

- -

SNP block format

-

- Each snp block in a BGEN v1.0 file consists of the following data in order. -

-
- - - - - - - - - - - - - - - - - - - - - - -
No. of bytesDescription
4The number of individuals the row represents, hereafter denoted N. - This is an integer encoded in two bytes.
1An unsigned integer S, indicating the length of the storage used for the - SNPID and RSID fields in the row.
1The length, SNPID_size of (the data part of) the SNPID string. - This must be between 0 and S.
SThe SNPID of the row. - Only the first SNPID_size bytes will be used.
1The length, RSID_size of (the data part of) the RSID string. - This must be between 0 and S.
SThe RSID of the row. - Only the first RSID_size bytes will be used.
1 - The chromosome on which the SNP is found, encoded as an unsigned 8-bit integer. - The encoding is: - - - - - - - -
1-22:SNP lies in the chromosome with the given number.
23SNP lies in the non pseudo-autosomal part of the X chromosome.
24:SNP lies in the non pseudo-autosomal part of the Y chromosome.
253:SNP lies in the pseudo-autosomal region of the X/Y chromosomes.
254:SNP lies in the mitochondrial DNA
255:Indicates the chromosome is unknown. We advise that this only be used for test data.
-
4The SNP position, encoded as an unsigned 32-bit integer.
1The length LAof the 'A' allele, encoded as an unsigned 8-bit integer.
LAThe B allele.
1The length LB fo the B allele, encoded as an unsigned 8-bit integer.
LBThe B allele.
PGenotype probability data for the SNP for each of the N individuals in - the cohort. If the CompressedSNPBlocks flag is not set, this field consists of P=6*N bytes representing the probabilities. - If CompressedSNPBlocks is set, this field contains a 32-bit unsigned integer specifying the length of the compressed data, - followed by the compressed data itself. See below for more details.
13 + 2*S + PTOTAL
-
-

-

SNP block probability data

-

- The probability data is listed as a sequence of 2-byte signed integers. These should be interpreted in triples, - the first member being the probability of AA, the second the probability of AB, the third the probability of BB. - Altogether these occupy 6*N bytes where N is the number of samples. These 6 * N bytes are written directly. -Alternatively, if the CompressedSNPBlocks flag is set in the header, these 6 * N bytes are first compressed using zlib. -The SNP block then contains a 4-byte integer representing the length of the compressed data followed by the compressed data itself. -

-

- To convert the stored 2-byte integers into probabilities, the following calculation should be performed: -

-
    -
  1. Convert the number into a floating-point format (e.g. float or double).
    2. -
  2. Divide by 10,000.
    3. -
-

- Note that the range of a two-byte unsigned integer is 0 - 65535 inclusive. Thus the resulting probabilities - can take on values between 0 and 6.5535 inclusive and are accurate to four decimal places. -

-

- Note: to convert a floating point number to the format, do the following: -

-
    -
  1. Check the number lies in the half-open interval [ 0, 6.55355 ).
    2. -
  2. Multiply by 10000 and round to the nearest integer.
    3. -
-

- All numbers are stored in little-endian (least significant byte first) order. -

- - \ No newline at end of file diff --git a/doc/html/index.html b/doc/html/index.html deleted file mode 120000 index 1596fc0cb..000000000 --- a/doc/html/index.html +++ /dev/null @@ -1 +0,0 @@ -bgen_format.html \ No newline at end of file diff --git a/doc/html/index.html b/doc/html/index.html new file mode 100644 index 000000000..eb3053bd0 --- /dev/null +++ b/doc/html/index.html @@ -0,0 +1,98 @@ + + + + + The BGEN format + + + + + + +
+
+ The BGEN format +
+ +
+ A compressed binary format for typed and imputed genotype data +
+ +
+ +
+

Introduction

+ +

+ Modern genetic association studies routinely employ data on tens to hundreds of thousands + of individuals, genotyped or imputed at tens of millions of markers genome-wide. Traditional + data formats based on text representation of these data - such as + the GEN + format output by IMPUTE, + or the Variant Call Format + - are sometimes not well suited to these data quantities. Indeed, for simple programs the time spent parsing + these formats can dominate program execution time. +

+

+ This page describes a binary GEN file format (the "BGEN" format) which aims to address these problems. + BGEN is a robust format that has been designed to have a specific blend of features that we believe make it + useful for this type of study. It is targetted for use with large, potentially imputed genetic datasets. + Key features include: + +

  • The ability store both directly typed and imputed data.
    • +
  • The ability to store both unphased genotypes and phased haplotype data.
    • +
  • Small file sizes through the use of efficient, variable-precision packed bit representations and compression.
    • +
  • The use of per-variant compression makes the format simple to index and easy to catalogue.
    • + +

    +

    + For example, the following plot shows the time taken to list variant identifying data - i.e. the genomic + position, ID fields and alleles - for various common formats (Y-axis), against file size (X axis), for a dataset + of 18,496 samples typed at 121,668 SNPs on chromosome 1. Both variants of BGEN defined below are shown. +

    +
    +
    + +
    +
    +

    + For PLINK binary (.bed) files, identifying data is + stored in a separate file (the .bim file) so the time is effectively zero. + For text-based formats there is a significant trade-off between the use of file compression and + read performance. BGEN stores + the entire dataset of 2,250 million genotypes in 334Mb, slightly over one bit per genotype, and in this test took 1.5s. +

    +

    + (Performance optimisation of all formats may of course be possible, so the above plot + will not represent the best possible timings, but should be regarded as illustrative.) +

    +

    + The BGEN format has been used in several major projects, including the + Wellcome Trust Case-Control Consortium 2, + the MalariaGEN project, and the ALSPAC study. + It has been adopted as the release format for genome-wide imputed genotypes + for the UK Biobank. +

    +
    +
    + Acknowledgements. The following people contributed to the design and implementation of the BGEN format: + +
    + + \ No newline at end of file diff --git a/doc/html/spec/latest.html b/doc/html/spec/latest.html new file mode 120000 index 000000000..194093f80 --- /dev/null +++ b/doc/html/spec/latest.html @@ -0,0 +1 @@ +v1.3.html \ No newline at end of file diff --git a/doc/html/bgen_format_v1.1.html b/doc/html/spec/v1.1.html similarity index 65% rename from doc/html/bgen_format_v1.1.html rename to doc/html/spec/v1.1.html index 5a89e993c..c49912393 100755 --- a/doc/html/bgen_format_v1.1.html +++ b/doc/html/spec/v1.1.html @@ -3,8 +3,8 @@ Gavin Band's webspace at the Wellcome Trust Centre for Human Genetics - + REL="stylesheet"> +
    @@ -20,90 +20,9 @@
    v1.1
    This page documents version 1.1 of the BGEN format. - A more recent version of this document is available - see - the latest BGEN specification. + A more recent version of this specification is available - see + here for details.
    -
    -
    -

    Introduction

    -

    Background

    -

    - Modern genetic association studies routinely employ data on tens to hundreds of thousands - of individuals, genotyped or imputed at tens of millions of markers genome-wide. Traditional - data formats based on text representation of these data - such as - the GEN - format output by IMPUTE, - or the Variant Call Format - - are sometimes not well suited to these data quantities. For simple programs the time spent parsing - these formats can dominate program execution time. -

    -

    - This page describes a binary GEN file format (the "BGEN" format) which aims to address these problems. - BGEN is a robust format that has been designed to have a specific blend of features that we believe make it - useful for this type of study. It is targetted for use with large, potentially imputed genetic datasets. - Key features include: - -

  • The ability store both directly typed and imputed data.
    • -
  • Small file sizes through the use of an efficient representation of probability data and compression.
    • -
  • The use of per-variant compression makes the format simple to index and easy to catalogue.
    • - -

    -

    - The BGEN format has been used in several major projects, including the - Wellcome Trust Case-Control Consortium 2 - and the MalariaGEN project. - It will be the release format for genome-wide genotype data for - the UK Biobank. -

    -
    -
    - Acknowledgements. The following people contributed to the design and implementation of the BGEN format: - -
    -
    -

    Tool support

    -
      -
    • QCTOOL can be used to read and write - BGEN files, and to convert them to other formats.
      • -
    • We have written a tool cat-bgen which can be used to efficiently - concatenate BGEN files. We found this useful for joining together chunks of imputed data after a genome-wide - imputation run.
      • -
    • SNPTEST has supported BGEN since - version 2.4.0.
      • -
    • PLINK 1.9 now includes support for BGEN.
      • -
    -

    A freely available C++ implementation of the BGEN format is available in the "genfile" sublibrary of QCTOOL, - available here.

    -
    -

    Change history

    -
    - -
    -
    -
    v1.1 (March 2012):
    -
    - BGEN format that is designed to cope with the long alleles present at indels and - structural variants in recent releases of the 1000 genomes project. Features - of this version are: -
      -
    • Support for biallelic SNPs and indels with alleles of arbitrary length (up to 232-1).
      • -
    • Store probabilities to at least 4 decimal places worth' of accuracy
      • -
    -
    -
    v1.0 (2009):
    -
    - The original BGEN format. This version is now deprecated and will be removed - from a future version of this spec; there probably aren't any files in the wild - in this format. -
    -

    Detailed specification

    diff --git a/doc/html/bgen_format_v1.2.html b/doc/html/spec/v1.2.html similarity index 63% rename from doc/html/bgen_format_v1.2.html rename to doc/html/spec/v1.2.html index 812c9f910..eda8d90cb 100644 --- a/doc/html/bgen_format_v1.2.html +++ b/doc/html/spec/v1.2.html @@ -4,9 +4,9 @@ The BGEN format - - - + + + @@ -24,176 +24,12 @@

    v1.2
    This page documents version 1.2 of the BGEN format. - A later version is available - see here. - This version is backward-compatible with the - earlier v1.1 format spec - - this means every v1.1-format BGEN file is also a valid v1.2-format file. - The v1.2 spec adds a new, more flexible layout for storing variant genotypes and haplotypes. - (See below for a full history of versions of this spec). -

    - Note: The UK Biobank full release imputed genotype data will be released in BGEN format, using - using 8 bits per probability and zlib compression, as described in this specification. - Phased haplotype data has also been released in BGEN format. -

    -

    - The UK Biobank interim release imputed genotype data was released in BGEN v1.1 format. -

    + A more recent version of this specification is available - see + here for details.
    -
    -

    Introduction

    -

    - Modern genetic association studies routinely employ data on tens to hundreds of thousands - of individuals, genotyped or imputed at tens of millions of markers genome-wide. Traditional - data formats based on text representation of these data - such as - the GEN - format output by IMPUTE, - or the Variant Call Format - - are sometimes not well suited to these data quantities. Indeed, for simple programs the time spent parsing - these formats can dominate program execution time. -

    -

    - This page describes a binary GEN file format (the "BGEN" format) which aims to address these problems. - BGEN is a robust format that has been designed to have a specific blend of features that we believe make it - useful for this type of study. It is targetted for use with large, potentially imputed genetic datasets. - Key features include: - -

  • The ability store both directly typed and imputed data.
    • -
  • The ability to store both unphased genotypes and phased haplotype data.
    • -
  • Small file sizes through the use of efficient, variable-precision packed bit representations and compression.
    • -
  • The use of per-variant compression makes the format simple to index and easy to catalogue.
    • - -

    -

    - For example, the following plot shows the time taken to list variant identifying data - i.e. the genomic - position, ID fields and alleles - for various common formats (Y-axis), against file size (X axis), for a dataset - of 18,496 samples typed at 121,668 SNPs on chromosome 1. Both variants of BGEN defined below are shown. -

    -
    -
    - -
    -
    -

    - For PLINK binary (.bed) files, identifying data is - stored in a separate file (the .bim file) so the time is effectively zero. - For text-based formats there is a significant trade-off between the use of file compression and - read performance. BGEN stores - the entire dataset of 2,250 million genotypes in 334Mb, slightly over one bit per genotype, and in this test took 1.5s. -

    -

    - (Performance optimisation of all formats may of course be possible, so the above plot - will not represent the best possible timings, but should be regarded as illustrative.) -

    -

    - The BGEN format has been used in several major projects, including the - Wellcome Trust Case-Control Consortium 2 - and the MalariaGEN project. - It has been adopted as the release format for genome-wide imputed genotypes - for the UK Biobank. -

    -
    -
    - Acknowledgements. The following people contributed to the design and implementation of the BGEN format: - -
    -
    -

    Software support

    -

    A freely available C++ implementation of the BGEN format is available - on bitbucket. This repository also contains a number of useful tools: -

    -
    -
    bgenix
    -
    A tool which provides random access to data in a BGEN file by creating an index.
    -
    cat-bgen
    -
    A program to efficiently concatenate BGEN files. Together with bgenix this effectively - enables map/reduce pipelines that operate in parallel on seperate genomic regions. - For example, we have found this useful for joining data into chromosomes after imputing genome-wide.
    -
    edit-bgen
    -
    A tool to (destructively) edit the BGEN header data.
    -
    rbgen
    -
    An R package that can be used to load data from an bgenix-indexed BGEN file into R.
    -
    -

    - In addition a set of example files and example programs, intended to demonstrate the API, are provided. -

    -

    - Bgen support has been also implemented in several other software packages, click on the links below for more information. -

    -
    - qctool v2 - SNPTEST - PLINK - Mega2 - LDSTORE - REGSCAN - BGENIE - Hail - BOLT-LMM -
    -

    - (Please contact me if your software supports BGEN and you'd like it added to this list.) -

    -
    -
    -

    Change history

    - -
    -
    -

    - A history of revisions of the v1.2 format spec is as follows: -

    -
      -
      BGEN v1.2 (November 2016):
      -
      - Major update extending the BGEN format to add: -
        -
      • Support for variable ploidy and explicit missing data.
        • - -
      • Support for multi-allelic variants (e.g. complex structural - variants).
        • - -
      • Allow for control over file size by supporting genotype probabilities - stored at configurable precision.
        • - -
      • Support for storing sample identifiers.
        • -
      - A draft version of this spec was published beginning May 2015. The following changes have been made since the earlier draft: -
        -
      • 2015-11-05 (v1.2 beta1): modified the treatment of missing data in Layout 2 (v1.2-style) variant data blocks.
        • -
      • 2016-03-21 (v1.2 beta2): modified the order of stored probabilities for samples with ploidy greater than 2; - clarified specification of the phased flag for samples with ploidy less than 2.
        • -
      -
      -
      BGEN v1.1 (March 2012):
      -
      - The first widely used version of the BGEN format. The UK Biobank interim imputed data was released in this format. - Relative to v1.0, this version is designed to cope with the long alleles present at indels and - structural variants in recent releases of the 1000 genomes project. Features - of this version are: -
        -
      • Support for biallelic SNPs and indels with alleles of arbitrary length (up to 232-1).
        • -
      • Store probabilities to at least 4 decimal places worth' of accuracy
        • -
      -
      -
      BGEN v1.0 (2009):
      -
      - The original BGEN format. This version is now deprecated and will be removed - from a future version of this spec; there probably aren't any files in the wild - in this format. -
      -
    -
    -

    Detailed specification

    Overview

    @@ -988,115 +824,5 @@

    Representation of probabilities

    We therefore renormalise input probabilities to sum to one.

    -

    Rationale and FAQ

    -
    -

    - Q. Should I use BGEN v1.1 or v1.2? Or something else? -

    -

    - A. The short answer is that we believe that for most purposes BGEN v1.2 is a - good choice for storage of hard-called or imputed genotypes. -

    -

    For a more detailed answer, the following table tabulates features of various different formats: - - - - - - - - - - - - - - - - - -
    PLINK binaryGENBGEN v1.1BGEN v1.2VCFBCF
    Supports unphased genotype calls✓✓*✓*✓✓✓
    Supports unphased genotype probabilities✓✓✓✓✓
    Supports NULL/outlier probability
    e.g. NULL class from CHIAMO / GenoSNP    		✓✓✓✓
    Supports non-diploid samples††✓✓‡✓‡
    Supports phased data?✓✓‡✓‡
    Supports multi-allelic variants✓✓✓
    Efficient representation?✓✓✓✓
    -

    - - *Hard-called genotypes are converted to probabilities in GEN and BGEN v1.1. - †By convention, males on the X chromosome are stored as homozygote females in GEN and BGEN v1.1. - ‡At the time of writing, the storage of genotype likelihoods and probabilities for non-diploid samples - and/or phased data in VCF/BCF is not fully specified. - -

    -

    - Thus BGEN v1.2 is appropriate except for storing genotype probabilities from cluster-based calles such as - CHIAMO - or GenoSNP, - which can assign nonzero probability to a NULL or outlier class. Use BGEN v1.1 or another format for these data. -

    - Another consideration over what to use is tool support. Support for BGEN v1.1 has been available for some time in - QCTOOL, SNPTEST and other packages including PLINK. Support for BGEN v1.2 is becoming available across a range of tools - mid-2016. We expect tool support for BGEN to continue to increase in future, driven in part by the use of - BGEN for the UK Biobank data releases and the availability of a reference implementation. -

    - Q. Why compress the data for each variant seperately? Doesn't this end up using more space? -

    -

    - A. Compressing each variant seperately has the advantage that the variant identifying data fields - - which are stored uncompressed in BGEN - can be efficiently accessed without decompressing the whole file. - It's true that theoretically higher rates of compression could be acheived by compressing as much data as possible. - However, for large cohorts, each variant has plenty of data to compress, so the difference is expected to be small. - (Alternative indexing approaches - like bgzip, which - compresses data in blocks - also incur a size overhead.) -

    -

    - Q. Why store the number of individuals on each row? Why store the number of alleles twice? Doesn't this waste space? -

    -

    - A. Yes, each repeated field wastes 4 bytes per variant. However, this is expected to be a tiny fraction of overall file size. - The inclusion of repeated fields makes parsing simpler (since parsers don't need to be stateful) and also provides a useful way - of testing that file structure is correct. -

    -

    - Q. (For Layout 2 variant data blocks) Why the choice of colex order of genotypes? -

    -

    - A. Several considerations motivated this choice - including simplicity of specification, ease of implementation, - and compatibility with established standards. -

    -

    - The colex order coincides with the order specified for - GL and GP fields for diploid samples in the VCF. (At the time of writing the VCF specification of this field - only applies to diploid samples). This makes it easy to convert between BGEN and VCF formats. -

    -

    - The chosen order has a useful 'nesting' property: adding an allele does not change the order of probabilities for - genotypes not carrying the new allele. More precisely, at a variant with K+1 alleles, genotypes - carrying only alleles among the first K appear earlier in the ordering than - those carrying the Kth allele - and with the same order as if the 'extra' allele wasn't present. - A practical consequence of this is that mapping of each genotype to the index of - the corresponding probability can be accomplished using a single lookup table that is independent of K - (though it does depend on the ploidy). We used such a lookup table in the - QCTOOL implementation to convert hard-called - genotypes to probabilities. -

    -

    - Q. (For Layout 2 variant data blocks) Why omit the last probability instead of the first? -

    -

    - A. The intention is to make parsing the file as simple and fast as possible. If we omitted the first probability, - parsers would have to read and store all the other probabilities before computing and emitting - the first probability. With the scheme described here, parsers can simply emit the probabilities as they are read from the file, - before finally emitting the last probability as one minus the sum of the stored probabilities. -

    - Q. (For Layout 2 variant data blocks) Why store dummy zero data for samples with missing genotypes? - Doesn't this increase file size unneccessarily? -

    -

    - A. - (Note this behaviour was changed in the beta version of the spec relative to the earlier draft.) - The intention is to make parsing the file as simple and fast as possible. One option for loading genotypes - from a BGEN file is simply to load the uncompressed genotype data into memory. Potentially, encoded genotypes could - then be used directly, e.g. as keys in a lookup table. Storing placeholder data for missing samples - makes this simpler to implement by maintaining a predictable index for the data for each sample within the encoded - representation. (We note this will be more complicated if ploidy varies across samples). -

    -
    diff --git a/doc/html/bgen_format_v1.3.html b/doc/html/spec/v1.3.html similarity index 62% rename from doc/html/bgen_format_v1.3.html rename to doc/html/spec/v1.3.html index 9f7e24254..7272af0d5 100644 --- a/doc/html/bgen_format_v1.3.html +++ b/doc/html/spec/v1.3.html @@ -4,9 +4,9 @@ The BGEN format - - - + + + @@ -19,187 +19,25 @@ A compressed binary format for typed and imputed genotype data
    +
    v1.3
    This page documents version 1.3 of the BGEN format. - This version is backward-compatible with the - earlier v1.2 and - v1.1 format specs - - this means every v1.2-format or v1.1-format BGEN file is also a valid v1.3-format file. - The v1.3 spec adds the ability to compress using zstandard - instead of zlib. - (See below for a full history of versions of this spec). -

    - Note: The UK Biobank full release imputed genotype data will be released in BGEN format, using - using 8 bits per probability and zlib compression (so compatible with the BGEN v1.2 format specification). - Phased haplotype data has also been released in BGEN format. -

    -

    - The UK Biobank interim release imputed genotype data was released in BGEN v1.1 format. -

    + A history of revisions can be found here.
    -
    -

    Introduction

    -

    - Modern genetic association studies routinely employ data on tens to hundreds of thousands - of individuals, genotyped or imputed at tens of millions of markers genome-wide. Traditional - data formats based on text representation of these data - such as - the GEN - format output by IMPUTE, - or the Variant Call Format - - are sometimes not well suited to these data quantities. Indeed, for simple programs the time spent parsing - these formats can dominate program execution time. -

    -

    - This page describes a binary GEN file format (the "BGEN" format) which aims to address these problems. - BGEN is a robust format that has been designed to have a specific blend of features that we believe make it - useful for this type of study. It is targetted for use with large, potentially imputed genetic datasets. - Key features include: - -

  • The ability store both directly typed and imputed data.
    • -
  • The ability to store both unphased genotypes and phased haplotype data.
    • -
  • Small file sizes through the use of efficient, variable-precision packed bit representations and compression.
    • -
  • The use of per-variant compression makes the format simple to index and easy to catalogue.
    • - -

    -

    - For example, the following plot shows the time taken to list variant identifying data - i.e. the genomic - position, ID fields and alleles - for various common formats (Y-axis), against file size (X axis), for a dataset - of 18,496 samples typed at 121,668 SNPs on chromosome 1. Both variants of BGEN defined below are shown. -

    -
    -
    - -
    -
    -

    - For PLINK binary (.bed) files, identifying data is - stored in a separate file (the .bim file) so the time is effectively zero. - For text-based formats there is a significant trade-off between the use of file compression and - read performance. BGEN stores - the entire dataset of 2,250 million genotypes in 334Mb, slightly over one bit per genotype, and in this test took 1.5s. -

    -

    - (Performance optimisation of all formats may of course be possible, so the above plot - will not represent the best possible timings, but should be regarded as illustrative.) -

    -

    - The BGEN format has been used in several major projects, including the - Wellcome Trust Case-Control Consortium 2 - and the MalariaGEN project. - It has been adopted as the release format for genome-wide imputed genotypes - for the UK Biobank. -

    -
    -
    - Acknowledgements. The following people contributed to the design and implementation of the BGEN format: - -
    -
    -

    Software support

    -

    A freely available C++ implementation of the BGEN format is available - on bitbucket. This repository also contains a number of useful tools: -

    -
    -
    bgenix
    -
    A tool which provides random access to data in a BGEN file by creating an index.
    -
    cat-bgen
    -
    A program to efficiently concatenate BGEN files. Together with bgenix this effectively - enables map/reduce pipelines that operate in parallel on seperate genomic regions. - For example, we have found this useful for joining data into chromosomes after imputing genome-wide.
    -
    edit-bgen
    -
    A tool to (destructively) edit the BGEN header data.
    -
    rbgen
    -
    An R package that can be used to load data from an bgenix-indexed BGEN file into R.
    -
    -

    - In addition a set of example files and example programs, intended to demonstrate the API, are provided. -

    -

    - Bgen support has been also implemented in several other software packages, click on the links below for more information. -

    -
    - qctool v2 - SNPTEST - PLINK - Mega2 - LDSTORE - REGSCAN - BGENIE - Hail - BOLT-LMM -
    -

    - (Please contact me if your software supports BGEN and you'd like it added to this list.) -

    -
    -
    -

    Change history

    - -
    -
    -

    - A history of revisions of the BGEN format spec is as follows: -

    -
      -
      BGEN v1.3 (January 2017):
      -
      -
    • Support for the zstandard compression library. - Tests indicate this has better performance both in terms of file size - and speed of reading and writing.
      • -
      -
      BGEN v1.2 (March 2016):
      -
      - Major update extending the BGEN format to add: -
        -
      • Support for variable ploidy and explicit missing data.
        • - -
      • Support for multi-allelic variants (e.g. complex structural - variants).
        • - -
      • Allow for control over file size by supporting genotype probabilities - stored at configurable precision.
        • - -
      • Support for storing sample identifiers.
        • -
      - A draft version of this spec was published beginning May 2015. The following changes have been made since the earlier draft: -
        -
      • 2015-11-05 (v1.2 beta1): modified the treatment of missing data in Layout 2 (v1.2-style) variant data blocks.
        • -
      • 2016-03-21 (v1.2 beta2): modified the order of stored probabilities for samples with ploidy greater than 2; - clarified specification of the phased flag for samples with ploidy less than 2.
        • -
      - -
      -
      BGEN v1.1 (March 2012):
      -
      - The first widely used version of the BGEN format. The UK Biobank interim imputed data was released in this format. - Relative to v1.0, this version is designed to cope with the long alleles present at indels and - structural variants in recent releases of the 1000 genomes project. Features - of this version are: -
        -
      • Support for biallelic SNPs and indels with alleles of arbitrary length (up to 232-1).
        • -
      • Store probabilities to at least 4 decimal places worth' of accuracy
        • -
      -
      -
      BGEN v1.0 (2009):
      -
      - The original BGEN format. This version is now unsupported. -
      -
    -
    -
    -

    Detailed specification

    +

    Overview

    A BGEN file consists of a header block, giving general infomation about the file, @@ -999,116 +837,6 @@

    Representation of probabilities

    We therefore renormalise input probabilities to sum to one.

    -

    Rationale and FAQ

    -
    -

    - Q. Should I use BGEN v1.1, v1.2, or v.1.3? Or something else? -

    -

    - A. The short answer is that we believe that for most purposes BGEN v1.2 and v1.3 is a - good choice for storage of hard-called or imputed genotypes. -

    -

    For a more detailed answer, the following table tabulates features of various different formats: - - - - - - - - - - - - - - - - - -
    PLINK binaryGENBGEN v1.1BGEN v1.2 / v1.3VCFBCF
    Supports unphased genotype calls✓✓*✓*✓✓✓
    Supports unphased genotype probabilities✓✓✓✓✓
    Supports NULL/outlier probability
    e.g. NULL class from CHIAMO / GenoSNP    		✓✓✓✓
    Supports non-diploid samples††✓✓‡✓‡
    Supports phased data?✓✓‡✓‡
    Supports multi-allelic variants✓✓✓
    Efficient representation?✓✓✓✓
    -

    - - *Hard-called genotypes are converted to probabilities in GEN and BGEN v1.1. - †By convention, males on the X chromosome are stored as homozygote females in GEN and BGEN v1.1. - ‡At the time of writing, the storage of genotype likelihoods and probabilities for non-diploid samples - and/or phased data in VCF/BCF is not fully specified. - -

    -

    - Thus BGEN v1.2 or v1.3 is appropriate except for storing genotype probabilities from cluster-based calles such as - CHIAMO - or GenoSNP, - which can assign nonzero probability to a NULL or outlier class. Use BGEN v1.1 or another format for these data. -

    - Another consideration over what to use is tool support. Support for BGEN v1.1 has been available for some time in - QCTOOL, SNPTEST and other packages including PLINK. Support for BGEN v1.2 is becoming available across a range of tools - mid-2016. We expect tool support for BGEN to continue to increase in future, driven in part by the use of - BGEN for the UK Biobank data releases and the availability - of a reference implementation. -

    - Q. Why compress the data for each variant seperately? Doesn't this end up using more space? -

    -

    - A. Compressing each variant seperately has the advantage that the variant identifying data fields - - which are stored uncompressed in BGEN - can be efficiently accessed without decompressing the whole file. - It's true that theoretically higher rates of compression could be acheived by compressing as much data as possible. - However, for large cohorts, each variant has plenty of data to compress, so the difference is expected to be small. - (Alternative indexing approaches - like bgzip, which - compresses data in blocks - also incur a size overhead.) -

    -

    - Q. Why store the number of individuals on each row? Why store the number of alleles twice? Doesn't this waste space? -

    -

    - A. Yes, each repeated field wastes 4 bytes per variant. However, this is expected to be a tiny fraction of overall file size. - The inclusion of repeated fields makes parsing simpler (since parsers don't need to be stateful) and also provides a useful way - of testing that file structure is correct. -

    -

    - Q. (For Layout 2 variant data blocks) Why the choice of colex order of genotypes? -

    -

    - A. Several considerations motivated this choice - including simplicity of specification, ease of implementation, - and compatibility with established standards. -

    -

    - The colex order coincides with the order specified for - GL and GP fields for diploid samples in the VCF. (At the time of writing the VCF specification of this field - only applies to diploid samples). This makes it easy to convert between BGEN and VCF formats. -

    -

    - The chosen order has a useful 'nesting' property: adding an allele does not change the order of probabilities for - genotypes not carrying the new allele. More precisely, at a variant with K+1 alleles, genotypes - carrying only alleles among the first K appear earlier in the ordering than - those carrying the Kth allele - and with the same order as if the 'extra' allele wasn't present. - A practical consequence of this is that mapping of each genotype to the index of - the corresponding probability can be accomplished using a single lookup table that is independent of K - (though it does depend on the ploidy). We used such a lookup table in the - QCTOOL implementation to convert hard-called - genotypes to probabilities. -

    -

    - Q. (For Layout 2 variant data blocks) Why omit the last probability instead of the first? -

    -

    - A. The intention is to make parsing the file as simple and fast as possible. If we omitted the first probability, - parsers would have to read and store all the other probabilities before computing and emitting - the first probability. With the scheme described here, parsers can simply emit the probabilities as they are read from the file, - before finally emitting the last probability as one minus the sum of the stored probabilities. -

    - Q. (For Layout 2 variant data blocks) Why store dummy zero data for samples with missing genotypes? - Doesn't this increase file size unneccessarily? -

    -

    - A. - (Note this behaviour was changed in the beta version of the spec relative to the earlier draft.) - The intention is to make parsing the file as simple and fast as possible. One option for loading genotypes - from a BGEN file is simply to load the uncompressed genotype data into memory. Potentially, encoded genotypes could - then be used directly, e.g. as keys in a lookup table. Storing placeholder data for missing samples - makes this simpler to implement by maintaining a predictable index for the data for each sample within the encoded - representation. (We note this will be more complicated if ploidy varies across samples). -

    -
    + \ No newline at end of file diff --git a/doc/html/style.css b/doc/html/style.css index d5c7bd003..babc2ab32 100755 --- a/doc/html/style.css +++ b/doc/html/style.css @@ -25,6 +25,34 @@ div.header { font-size: 15px ; } +nav { + clear: both ; + position: relative ; + font: sans-serif ; + font-size: 20px ; + padding: 0px ; + margin: 0px ; + background-color: #dddddd; + border-radius: 2px ; +} + +nav > ul { + position: relative; + list-style: none ; + padding-top: 0px ; + padding-bottom: 0px ; + margin-top: 0px ; + margin-bottom: 0px ; + text-align: left ; +} + +nav > ul > li { + display: inline-block ; + min-width: 5em ; + text-align: left ; + clear: none ; +} + #overview { clear: both ; } @@ -245,6 +273,3 @@ div.logo_container + p { clear: both; padding-top: 20px ; } - - - From a855a8a2c5b92a555df5810e9009ccf1fdfea95a Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Thu, 12 Sep 2019 10:11:48 +0000 Subject: [PATCH 05/12] bgenix: output multiple IDs with semicolon, not comma separator cf issue --- Makefile | 21 ++++++++- apps/bgenix.cpp | 2 +- doc/html/history.html | 95 +++++++++++++++++++++++++++++++++++++++++ doc/html/index.html | 9 ++++ doc/html/paper.html | 66 ++++++++++++++++++++++++++++ doc/html/software.html | 93 ++++++++++++++++++++++++++++++++++++++++ doc/html/spec/v1.2.html | 10 +++++ doc/html/spec/v1.3.html | 10 +++++ 8 files changed, 303 insertions(+), 3 deletions(-) create mode 100644 doc/html/history.html create mode 100644 doc/html/paper.html create mode 100644 doc/html/software.html diff --git a/Makefile b/Makefile index 9b5804165..a7b0ac865 100644 --- a/Makefile +++ b/Makefile @@ -1,3 +1,20 @@ -FLAGS = -g -std=c++11 -Igenfile/include -lz -bgen_to_vcf: example/bgen_to_vcf.cpp +FLAGS = -g -std=c++11 -lz \ +-I genfile/include \ +-I db/include \ +-I 3rd_party/boost_1_55_0 \ +-I 3rd_party/zstd-1.1.0 \ +-I 3rd_party/zstd-1.1.0/lib \ +-I 3rd_party/zstd-1.1.0/lib/common \ +-I 3rd_party/zstd-1.1.0/lib/compress \ +-I 3rd_party/zstd-1.1.0/lib/decompress \ +-I 3rd_party/sqlite3 \ +-I include/3rd_party/sqlite3 \ +-D SQLITE_ENABLE_COLUMN_METADATA \ +-D SQLITE_ENABLE_STAT4 \ +-D SQLITE_MAX_EXPR_DEPTH=10000 \ +-D SQLITE_USE_URI=1 \ +-Wno-unused-local-typedefs \ +-fPIC -O3 + +bgen_to_vcf: example/bgen_to_vcf.cpp $(wildcard 3rd_party/zstd-1.1.0/*.o) $(wildcard 3rd_party/sqlite3/*.o) g++ ${FLAGS} -o build/bgen_to_vcf example/bgen_to_vcf.cpp src/*.cpp diff --git a/apps/bgenix.cpp b/apps/bgenix.cpp index 8915a982e..2ce5e618f 100644 --- a/apps/bgenix.cpp +++ b/apps/bgenix.cpp @@ -816,7 +816,7 @@ struct IndexBgenApplication: public appcontext::ApplicationContext assert( alleles.size() > 1 ) ; std::cout << chromosome << "\t" << position - << "\t" << rsid << "," << SNPID + << "\t" << rsid << ";" << SNPID << "\t" << alleles[0] << "\t" ; for( std::size_t j = 1; j < alleles.size(); ++j ) { diff --git a/doc/html/history.html b/doc/html/history.html new file mode 100644 index 000000000..a6c4cc32d --- /dev/null +++ b/doc/html/history.html @@ -0,0 +1,95 @@ + + + + + + + + The BGEN format + + + + + + +
    +
    + The BGEN format +
    + +
    + A compressed binary format for typed and imputed genotype data +
    + +
    + +
    +

    History of revisions

    +
    +

    + A history of revisions of the BGEN format specification is as follows: +

    +
      +
      BGEN v1.3 (January 2017): link to spec
      +
      +
    • Support for the zstandard compression library. + Tests indicate this has better performance both in terms of file size + and speed of reading and writing.
      • +
      +
      BGEN v1.2 (March 2016): link to spec
      +
      + Major update extending the BGEN format to add: +
        +
      • Support for variable ploidy and explicit missing data.
        • + +
      • Support for multi-allelic variants (e.g. complex structural + variants).
        • + +
      • Allow for control over file size by supporting genotype probabilities + stored at configurable precision.
        • + +
      • Support for storing sample identifiers.
        • +
      + A draft version of this spec was published beginning May 2015. The following changes have been made since the earlier draft: +
        +
      • 2015-11-05 (v1.2 beta1): modified the treatment of missing data in Layout 2 (v1.2-style) variant data blocks.
        • +
      • 2016-03-21 (v1.2 beta2): modified the order of stored probabilities for samples with ploidy greater than 2; + clarified specification of the phased flag for samples with ploidy less than 2.
        • +
      + +
      +
      BGEN v1.1 (March 2012): link to spec
      +
      + The first widely used version of the BGEN format. The UK Biobank interim imputed data was released in this format. + Relative to v1.0, this version is designed to cope with the long alleles present at indels and + structural variants in recent releases of the 1000 genomes project. Features + of this version are: +
        +
      • Support for biallelic SNPs and indels with alleles of arbitrary length (up to 232-1).
        • +
      • Store probabilities to at least 4 decimal places worth' of accuracy
        • +
      +
      +
      BGEN v1.0 (2009):
      +
      + The original BGEN format. This version is now unsupported. +
      +
    +
    + + + \ No newline at end of file diff --git a/doc/html/index.html b/doc/html/index.html index eb3053bd0..e31288b7b 100644 --- a/doc/html/index.html +++ b/doc/html/index.html @@ -3,6 +3,15 @@ + + + The BGEN format diff --git a/doc/html/paper.html b/doc/html/paper.html new file mode 100644 index 000000000..65b572038 --- /dev/null +++ b/doc/html/paper.html @@ -0,0 +1,66 @@ + + + + + + + + The BGEN format + + + + + + + +
    +
    + The BGEN format +
    + +
    + A compressed binary format for typed and imputed genotype data +
    + +
    + +
    +

    BGEN paper

    +

    + Our paper describing the motivation, design, and performance of the BGEN format + has been published on bioArxiv. + If you make use of BGEN in your project beyond simple application , please cite: +

    +
      +
    • + Gavin Band and Jonathan Marchini, "BGEN: a binary file format for imputed genotype and haplotype data", bioArxiv (2018), https://doi.org/10.1101/308296 +
      • +
    +

    UK Biobank paper

    +

    + Our paper describing the UK Biobank data resource has now been published in Nature. + If you make use of the UK Biobank genotype data resource, please cite: +

    +
      +
    • + Bycroft, Freeman, Petkova et al, "The UK Biobank resource with deep phenotyping and genomic data", Nature (2018), https://doi.org/10.1038/s41586-018-0579-z +
      • +
    +
    + + \ No newline at end of file diff --git a/doc/html/software.html b/doc/html/software.html new file mode 100644 index 000000000..709f1573f --- /dev/null +++ b/doc/html/software.html @@ -0,0 +1,93 @@ + + + + + + + + The BGEN format + + + + + + + +
    +
    + The BGEN format +
    + +
    + A compressed binary format for typed and imputed genotype data +
    + +
    + +
    +

    Software support

    +

    + For command-line users: BGEN support has been implemented in several software packages, click on the links below for more information. +

    +
    + qctool v2 + SNPTEST + PLINK + Mega2 + LDSTORE + REGSCAN + BGENIE + Hail + BOLT-LMM + FINEMAP + STITCH + bgenix +
    +

    + For R users: The rbgen package can be used to load data directly into R. +

    +

    + For python users: A number of python solutions have been developed, + see e.g. the bgen-reader library or the pybgen library. +

    +

    + (Please contact me if your software supports BGEN and you'd like it added to this list.) +

    + +

    For developers: A freely available C++ implementation of the BGEN format is available + on bitbucket. This repository also contains a number of useful tools: +

    +
    +
    bgenix
    +
    A tool which provides random access to data in a BGEN file by creating an index.
    +
    cat-bgen
    +
    A program to efficiently concatenate BGEN files. Together with bgenix this effectively + enables map/reduce pipelines that operate in parallel on seperate genomic regions. + For example, we have found this useful for joining data into chromosomes after imputing genome-wide.
    +
    edit-bgen
    +
    A tool to (destructively) edit the BGEN header data.
    +
    +

    + In addition a + set of example files and programs, + intended to demonstrate the API, are provided. +

    + +
    + + \ No newline at end of file diff --git a/doc/html/spec/v1.2.html b/doc/html/spec/v1.2.html index eda8d90cb..a825660b9 100644 --- a/doc/html/spec/v1.2.html +++ b/doc/html/spec/v1.2.html @@ -3,12 +3,22 @@ + + + The BGEN format +
    diff --git a/doc/html/spec/v1.3.html b/doc/html/spec/v1.3.html index 7272af0d5..ecfd753e2 100644 --- a/doc/html/spec/v1.3.html +++ b/doc/html/spec/v1.3.html @@ -3,12 +3,22 @@ + + + The BGEN format +
    From 59a74cc089317de848dcd9662a3192f954cb530f Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Thu, 12 Sep 2019 10:21:06 +0000 Subject: [PATCH 06/12] bgenix: use semicolon, not comma to seperate IDs, cf issue --- apps/bgenix.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apps/bgenix.cpp b/apps/bgenix.cpp index 8915a982e..2ce5e618f 100644 --- a/apps/bgenix.cpp +++ b/apps/bgenix.cpp @@ -816,7 +816,7 @@ struct IndexBgenApplication: public appcontext::ApplicationContext assert( alleles.size() > 1 ) ; std::cout << chromosome << "\t" << position - << "\t" << rsid << "," << SNPID + << "\t" << rsid << ";" << SNPID << "\t" << alleles[0] << "\t" ; for( std::size_t j = 1; j < alleles.size(); ++j ) { From c5d597d0154364ffc330ffd837a1304082a2fac7 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Thu, 12 Sep 2019 10:27:03 +0000 Subject: [PATCH 07/12] Bump to v1.1.5 --- wscript | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wscript b/wscript index f59428540..c4a262eae 100644 --- a/wscript +++ b/wscript @@ -2,7 +2,7 @@ import platform, os.path srcdir="." APPNAME = "bgen" -VERSION = "1.1.4" +VERSION = "1.1.5" def options( opt ): opt.load( 'compiler_cxx' ) From e19cba884e2d1baac391af7bda483df476c939e0 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Thu, 12 Sep 2019 10:30:28 +0000 Subject: [PATCH 08/12] bgenix -vcf: only output unique IDs --- apps/bgenix.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apps/bgenix.cpp b/apps/bgenix.cpp index 2ce5e618f..3c0200244 100644 --- a/apps/bgenix.cpp +++ b/apps/bgenix.cpp @@ -816,7 +816,7 @@ struct IndexBgenApplication: public appcontext::ApplicationContext assert( alleles.size() > 1 ) ; std::cout << chromosome << "\t" << position - << "\t" << rsid << ";" << SNPID + << "\t" << rsid << ( (SNPID == rsid) ? "" : (";" + SNPID)) << "\t" << alleles[0] << "\t" ; for( std::size_t j = 1; j < alleles.size(); ++j ) { From 07f6a725ec8b0aed9c38ccd2cef9fc3ec8fb0105 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Thu, 12 Sep 2019 10:33:18 +0000 Subject: [PATCH 09/12] Pull bgenix vcf semicolon fix from master branch --- apps/bgenix.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apps/bgenix.cpp b/apps/bgenix.cpp index 2ce5e618f..3c0200244 100644 --- a/apps/bgenix.cpp +++ b/apps/bgenix.cpp @@ -816,7 +816,7 @@ struct IndexBgenApplication: public appcontext::ApplicationContext assert( alleles.size() > 1 ) ; std::cout << chromosome << "\t" << position - << "\t" << rsid << ";" << SNPID + << "\t" << rsid << ( (SNPID == rsid) ? "" : (";" + SNPID)) << "\t" << alleles[0] << "\t" ; for( std::size_t j = 1; j < alleles.size(); ++j ) { From 5bcbd97729cb45ff4d4a7fe642fd6dd927472bb1 Mon Sep 17 00:00:00 2001 From: "maarten@oyat.nl" Date: Wed, 15 Jan 2020 18:00:27 +0000 Subject: [PATCH 10/12] syntax python 2 script was not compatible with python3. updated waf to version 2.0.19 --- waf | 15 +++++++++------ wscript | 20 ++++++++++---------- 2 files changed, 19 insertions(+), 16 deletions(-) diff --git a/waf b/waf index a42ba919f..b97424a91 100755 --- a/waf +++ b/waf @@ -32,13 +32,13 @@ POSSIBILITY OF SUCH DAMAGE. import os, sys, inspect -VERSION="2.0.6" -REVISION="f8aee10f7730da942389d88501d489e8" +VERSION="2.0.19" +REVISION="597b128bf9f9d1a665be0bd3cba5812c" GIT="x" INSTALL='' -C1='#0' -C2='#/' -C3='#.' +C1='#2' +C2='#-' +C3='#%' cwd = os.getcwd() join = os.path.join @@ -140,6 +140,9 @@ def find_lib(): if name.endswith('waf-light'): w = test(base) if w: return w + for dir in sys.path: + if test(dir): + return dir err('waf-light requires waflib -> export WAFDIR=/folder') dirname = '%s-%s-%s' % (WAF, VERSION, REVISION) @@ -165,5 +168,5 @@ if __name__ == '__main__': Scripting.waf_entry_point(cwd, VERSION, wafdir) #==> -#BZh91AY&SY68fOE# 0(b wzۡ#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#._.Ԫ̱!vԠ%6JMbF3}ii݇im<^-bP/n۽q=guҐ ]3!nkϧ|t{Ƕ6vwoowi"{ly#.#.' z}#.8v zˠ{WV(nWIO@:HZ$#.EJ@^ڭhXAI5k*^a>oouǽIz\NkT[X۾kg#..l屽[kGv;o{z{]ϋ紛vmپ76ݧtsvhzr$#0AH#fjTn{gy^yc+mѬ;gZzdT)=h#.!PIT@x#/l)Qe/{5*& S/n4PI$=>1K#.js0]ހ>wl7;IzǶ<=Jo tӍqӢS|;s}}mamM\\{_osSٹ[׷m:[}:5^>:|O'F:{wo]Jvj>lfv̦Uu&1̳NNtMt{͇sǮxQE(A(UEPNmfvJt֧e.zh0͝(zէm soIOkw{u3#. z܈#.:;vnUsk=g'Ll[=4zcU%+iΈ}9W^^oy UAyN&;K^݁Q糾j-qoN壧q7=>eգIҭ*wnvV^9ogu;{#R]wΙ;+ֹ87]mO^u >j-#.#.gmt;]k˾v{yVDl{'gg}@zM&{c]n:nݠŔ(lKGV#/c=olڕދymZcAGpȶd˜`;(+9roGFM#.#.4hi14hSȍHHM&CjzM3==(%4A @L Mz#.#.#.#.#. 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Ȟ_'DM}KAE/PEg^dpCOw͇AnO컉@%A[xu8ftG bIV( ?I-xz篩Q d.PlPxeP+1?5K!QQ‹,\tgQ yg.fa{59v: ,+0/l5Ҿۼ#$ޢZZBAuݘ8*$%^ֈ.xp>#-;cѩMNOi$H'UU:T{>@)„* #<== diff --git a/wscript b/wscript index 2f458a294..7e7769d62 100644 --- a/wscript +++ b/wscript @@ -2,7 +2,7 @@ import platform, os.path srcdir="." APPNAME = "bgen" -VERSION = "1.2-dev" +VERSION = "1.1.5" def options( opt ): opt.load( 'compiler_cxx' ) @@ -30,7 +30,7 @@ def configure( cfg ): cfg.check_cxx( lib='dl', uselib_store='dl', msg = 'dl' ) def build( bld ): - print "Creating %s build..." % bld.options.mode + print ("Creating %s build..." % bld.options.mode ) bld( rule = """printf '#ifndef BGEN_REVISION_HPP\n#define BGEN_REVISION_HPP\nnamespace globals {\n\tchar const* bgen_version = \"%%s\" ;\n\tchar const* const bgen_revision = \"%%s\" ;\n}\n#endif\n' `echo """ + VERSION + "` `hg parents --template={node}` > ${TGT}""", always = True, @@ -63,7 +63,7 @@ class ReleaseBuilder: def makedirs( self, path ): try: os.makedirs( path ) - except os.error, e: + except os.error as e: pass def create_pkgname_stub( self, packageName, includePlatform = True ): @@ -99,9 +99,9 @@ class ReleaseBuilder: tarballPath = os.path.join( workingdir, tarball ) process = subprocess.Popen( [ 'tar', '-czf', tarball, source ], cwd = workingdir ) process.wait() - print 'Created %s release tarball in "%s"' % ( name, tarball ) - print "Contents are:" - print subprocess.Popen( [ 'tar', '-tzf',tarballPath ], stdout = subprocess.PIPE ).communicate()[0] + print ('Created %s release tarball in "%s"' % ( name, tarball )) + print ("Contents are:") + print (subprocess.Popen( [ 'tar', '-tzf',tarballPath ], stdout = subprocess.PIPE ).communicate()[0]) return tarball def build_rbgen( self ): @@ -191,13 +191,13 @@ class ReleaseBuilder: def release( bld ): - print "Building bgen release tarball..." + print ("Building bgen release tarball...") release = ReleaseBuilder( APPNAME, VERSION ) result = release.build_bgen() - print "Created %s release tarball in \"%s\"" % ( 'bgen', result ) + print ("Created %s release tarball in \"%s\"" % ( 'bgen', result )) def build_rbgen( bld ): - print "Building rbgen source package tarball..." + print ("Building rbgen source package tarball...") release = ReleaseBuilder( APPNAME, VERSION ) result = release.build_rbgen() - print "Created %s release tarball in \"%s\"" % ( 'rbgen', result ) + print ("Created %s release tarball in \"%s\"" % ( 'rbgen', result )) From a096db9610c5a27d4e466f4ea039595b75bc8c46 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Wed, 15 Jan 2020 21:07:52 +0000 Subject: [PATCH 11/12] Fix Issue #39 and update CHANGELOG. --- CHANGELOG.md | 25 +++++++++++++++++++++++++ R/package/src/load.cpp | 2 +- 2 files changed, 26 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 18ce9f58f..b9e80b863 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,31 @@ History ==== +15 January 2020 +---- +v1.1.5 release. Changes are: + +- incorporate fix from Maarten Kooyman to build using Python 3. +- fix issue #39 + +7 August 2018 +---- +v1.1.4 release. Update to fix sample subset issue with BGEN v1.1. + +2 May 2015 +----- +v1.1.3 release. The main changes are: + +- The rbgen R package, which gets data from indexed BGEN files into R, is has several improvements - it's easier to install, and has additional features (see below). +- New, improved bgenix vcf output - now up to 50X faster. +- Further performance improvements and resolution of a number of issues across the library. + +To accompany this we have written a paper which is now available on bioArxiv: https://doi.org/10.1101/308296. + +13 July 2017 +---- +v1.0 release + 7 July 2016 ---- diff --git a/R/package/src/load.cpp b/R/package/src/load.cpp index bdfcc7f51..0dbb75749 100644 --- a/R/package/src/load.cpp +++ b/R/package/src/load.cpp @@ -67,7 +67,7 @@ namespace { // Called once per sample to determine whether we want data for this sample bool set_sample( std::size_t i ) { - if( m_requested_sample_i->first == i ) { + if( m_requested_sample_i != m_requested_samples.end() && m_requested_sample_i->first == i ) { m_storage_i = m_requested_sample_i->second ; ++m_requested_sample_i ; #if DEBUG From 905bd6d61ebe714a43829cfa9c1fec2ade1fb1e4 Mon Sep 17 00:00:00 2001 From: "gavin.band@well.ox.ac.uk" Date: Wed, 15 Jan 2020 21:08:25 +0000 Subject: [PATCH 12/12] Added example/example.8bits.bgen.bgi --- example/example.8bits.bgen.bgi | Bin 0 -> 11264 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 example/example.8bits.bgen.bgi diff --git a/example/example.8bits.bgen.bgi b/example/example.8bits.bgen.bgi new file mode 100644 index 0000000000000000000000000000000000000000..bd2a8de41bd3926b11b11b3a4d95899c83c6dec0 GIT binary patch literal 11264 zcmeI14RBS(6~}kaf+SE15tNUR@Te$61AX7`g^J|`Vh9ETAqW}7_<#p_m=N+oA&g*% zh+t_O7+OK84J}%bDIddFfubN_k*Tdfts=Dus8p#{K&0TP({t`_@a&DYx-oiiO#1^J>-IrzVCzW$dh&^R61bxTi|_g`NZpIni+JzkTH&#W^))X?I*SV^9z zB$iv4=P|$Z^!IqCl-E>MR@GKjCOjp16G}Xzitu|}VPUq%GpnjLS(mJu=_wdx{l2C) zIknY?XU?vioTw?QnpPICs7O>KYTcCnwXYSZfA2TH*UrHaRa* zmYi8OxxTKo*XZJck+I@Z&uw|7p8lWBF#F1svOP43Y>ydK%Y{GN^Lf@;S)TC)CBuux zm3WGa#up4*I83(dmXRSFCps%VGEowqcS|g=m$#PjJy|SygBwiDH#5(bSm?1`rUa4s+y;CQU z;Pr_m+l$8*3@ZzSV)^my0Kc-tMTfK)jOCYA1LRv`!`oU6#PTQY1Gyj3p!s~+xX{+w9;xEzp=bFK0&twm$` zW77dLxt5%(wMZ;~^g@7#xt3_sS~!+J@+3er*W&B7hAVU1dVn0RP1>V1T$q9nKt9Q} z(xY0#b;&;l(1UB^&T0+UC2ttO&$w2cqBUHXp_u?TaBY-FYq&148$e#-+K8y5`EXsn z-yh_sT)TC&)^J@0w|A{eZn@TQT?Rc0P{Fxd8nlM%65S8-7}o}^(i*Ny=x+dj=URA+ z)^J?{vjNJv=6_ymxGvrk06*p0z!O@-bs6{|!0lYS@sieXU9yK_5E>0rp?!vqWJQrI z$Le*D;(Wx(5df?46RFlG`szDHaO7hDVSq4xqFpB5BcoF%=N@9)Rx^H_xU9Ms;3oXY zRd^F<`N(`}W`RSMx6KF0#ZP!Fn_*GsBT<~Fc%=u*B8BVXz2S}?#tDga=rIXD(UyDU zCbfqTry{d90DPBj(o!petUiR;b(md8*maa$=X`eU^RjDJe|)U|_^AFEUmx@JF<&3^ z^)X)`^Yt-bKlAl7UqAEpGhaXR^)p{T^Yt@dKlAl7-vILsFy8?44KUvT^9?ZH0P_tn z-vILsFyA2a4Km*#^9?fJAoC3}-yri1GT$Kc4Km*l^9?cI5c3T&-w^W+G2amL4Kd#k z^9?cIF!K#F-!StHGv6@t4Kv>`^9?iKF!K#F-w5-KFy9FCjWFK`^Nldy2=k3F-w5-K zFyH7EU%%Jy9pLp1@C7|S|Dd3MP$)`y`&E3k$D8yKBZNAo4yX<4$7+@ury{Bsd%~|2jDg6mW8GUQ6=oR z1>|K;y88ns2dy?FmRZ^NAy8HabaxLKyD=Z9odIPG@kt!@+K| z92K=bNdW4uSNd<4r3R$v>bL;+EgbB!#8FYpyaZ6q!A@%pNWs+sH=dSbr)Eb*t=B&R zI&iSV4g*qbrThb+k~?xhBgE0@#bVu$6dGtT-`uVt9?~Qomy3YihtnZ;`9H1E&T#XCK zN%x6?le2w>q-?ph9N-B~y3Z4wtS-srgGAKe&S?tsv#+c{6W_#$$h%w z>@6RSJX+hUp=OlsH7@X15{@?hwlKMgjG-vcferqfRt~_=j3|16!!olrC0n`JS6JH z#Lvxs92C6`(C43hqn%NOa3RD44FHEMb$7X=263|D{yKnfS%u?w3-yeGG^5%}AkSFv z@AQ$9RB_)!WHA)j2x= z$}DzWnqetNrk(|Ljm56(tjCOM-6l{SEVenzu#_c}e}vV*Vw?3QA&6?t9Ds<$u8A3z z^5m`xfIb$xM(-1XsLmP<(9dF5m1;IXnKCI1%3iBgdaFQc#RX7zSnSGb!%}2TOaT~Z z`L3Mh$N^Mm9LMCf*ruh1rHVVg5!7OfZPFWt0IJi=K;3Jx%hno}YHrB_P;D%Bncg!5 zP@OsvMT=ds!>|-rV@?CCvRLZ8 zfE%r`yjP&dLT@YNO5BUYEx6UY3=2LJH!uavie&)ZEcnb_+L@}&THJPJS@7w44TmUV znsNa~Sn%n&j!dff#aefIomy^S3Yj0_QQ|ENKGmdQDn@Hog6e2FAKzeLikSyTqin&) z*J~J6v3fD6Z(H!OXAMk2^S~Z}CJR2cN5iO!pW(iDjRn8_s(~qL?#Gu{Kd|7Jk7^iI zu@Y-lr3D{3XJ87O#)|+Y7JTHahEWwO@~|aa@QbMirh3$H5MY1>znG$7R7KNZfD{Y< zLmvZELAvJ%sDD}TA3PeS2wOH6)N>YmAjiNIVe?i3++x88q8dh3;In}K7QAnafhoe~ zb^%yu!L9n41@BI3m>Qa#eG0&5!C!g1`|LgAQ>%?LMObwV;3>=bsa1{~qzGHsA7Dj$ zwHW(9=Ko2||8-wF`zxttd_n$8?-s`_Lb>n)Zn)awM+djO?v(vc>XAk$oVSk!SgQ7k z%$5ynu1U%fJ+oTQUFdwBQWgsUj4S zdwvd(X2CsT2BwJITmLR zm-pb4v|xEi!&LLOVuIhmVe!d32Bw<#=nJ5>a9DiuwuY(ZZR!nbwgrDA4NMWXW-`DG z3;sxGm?CWBWw-Oi9tNfeTRjX^rUhT@u3?I>^*_f=3HHy-D~XYPP{R>gu$`~rA6MA3 z5a)g7))apawE-An-TKS+T_VAAb%7-lzD|CBsq|=;xb5k@YeDozQBRa-M#G zITSjVu?8Hr*g5(MS?ie57#O^ zzW4T7v-NJ(v!$9RpT;ryEwWWbwBS|`e!m50KkwX|!a^LxrP^e{t;?we_dlUwT8#tk z0OnY5-^*s$lqpZ*QD(j+7oF2`l(O*f36NG7mPKbBnN;!m%>dT6MHZ$SnC|_ja{%vK z11n6?Fg=LZ@L*uIa5=n>fhh}L2m(B9!NWZorss4Fx9?Tfu!rRsn6mKT^`JUgu>IFG z9G3+T8Dn6|vjZ8pF|ptwqqQ^D`M=;RfwwI9=A?nC&hN)9(NPP&xm?3k=Z|2WueIRl zLIYEs-+LoKx&=oYG)#5=(1Wg%lnk!caD?jo?jrybEI7Ezkx3PQ^5I)m%Kx6?bW8tV ztfs31=%sFwpQw)VIJ_@+!(rJB+vGy{shkXR8 z;3ZJjxlT6j&?`tKNuIk8V2njCIBaCf@b`a+FM}+3p6NMMl;pd(hi_}ibEKguliofF z>M={M?O|lfmD9La?rzCdJ|j~$yop)7*OKopFfzsasjj#+vE=D-BU415NCWIjyiiZ6 zH!{WS-_B!`x8$ zc(%3FvL>xkj=s|c