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A complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics

License: GNU General Public License v2.0

Makefile 1.77% Python 2.07% C 96.12% Shell 0.04%

hpg-variant's People

Contributors

cyenyxe avatar gemalm3 avatar j-coll avatar jmmut avatar pescobar avatar

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Forkers

gemalm3 jlra cyenyxe charol daviddeunaa ahorvath wojcieszek-michal igalan j-coll jmmut pescobar abushoy jpdna mrg7 ebivariation srikanthkris gerbenvoshol

hpg-variant's Issues

Merging tool should accept a list of sorted chromosomes/contigs

Currently, the merging tool checks the order of chromosomes by querying CellBase. This makes impossible to merge species that have not been previously stored, such as those without a reference genome.

Since the files must still be sorted, the merging tool should accept a list of chromosomes/contigs in plain text format for checking this ordering.

VCF validator

Implement a tool that validates VCF files. Validation must not be run only in a per-row basis, but also considering context (multi-line positions, pedigree files, etc.)

Problem with installation in ubuntu

$ sudo apt-get install libconfig8 libcurl4-openssl-dev libgsl0ldbl libxml2 zlib1g
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package libgsl0ldbl is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
However the following packages replace it:
libgsl2 libgsl2:i386

E: Unable to locate package libconfig8
E: Package 'libgsl0ldbl' has no installation candidate

Looks like the required dependencies (old ones) aren't able to fit into the new ubuntu system. Is that the case?

hpg-var-vcf crashes loading config file

hpg-var-vcf crashes loading config file:

$ hpg-var-vcf aggregate -v /media/data/oldData/data/controls/1000genomes/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz --out test --outdir .                                                                        0 [Fri Feb 20, 11:22:54]
Fri Feb 20 11:23:25 2015    INFO    src/hpg_variant_utils.c [180] in retrieve_config_file(): Configuration file is in path /etc/hpg-variant/hpg-variant.conf
Fri Feb 20 11:23:25 2015    WARN    src/vcf-tools/aggregate/aggregate_options_parsing.c [132] in verify_aggregate_options(): Input PED file not specified: not all statistics can be calculated.
Fri Feb 20 11:23:25 2015    INFO    src/vcf-tools/aggregate/aggregate_runner.c [52] in run_aggregate(): About to retrieve statistics from VCF file...
Fri Feb 20 11:23:25 2015    INFO    src/hpg_variant_utils.c [311] in get_output_file(): Output file will be saved in path ./test
Fri Feb 20 11:23:25 2015    INFO    src/vcf-tools/aggregate/aggregate_runner.c [163] in run_aggregate(): Output filename = ./test
Fri Feb 20 11:23:25 2015    INFO    lib/bioinfo-libs/bioformats/vcf/vcf_reader.c [307] in vcf_gzip_read_and_parse(): Records read = 2
Fri Feb 20 11:23:25 2015    INFO    src/vcf-tools/aggregate/aggregate_runner.c [97] in run_aggregate(): Batch 0 reached by thread 3 - 2/2000 records 
Fri Feb 20 11:23:25 2015    INFO    src/hpg_variant_utils.c [180] in retrieve_config_file(): Configuration file is in path (null)
hpg-var-vcf: src/vcf-tools/aggregate/aggregate_runner.c:232: add_aggregator_header: Assertion `ret_code' failed.
[1]    19064 abort (core dumped)  hpg-var-vcf aggregate -v  --out test --outdir .

Reduce size of repository

The size of the repository is really big (about 160 MB). This should be reduced, probably by removing some test files that got lost in the revision tree.

Instructions for mac install?

Hi, hpg-variant looks like a good option for processing vcfs in my research. I noticed that install/compile instructions are only available for Debian and Fedora. Could you please give me some insight as to how to install on mac/unix? That would be great. Thanks.

Cannot build on CentOS 6.6

I'm unable to build hpg-variant v1.0. on a CentOS 6.6 machine. I followed the instructions stated in the README, but the build process failed at the second stage.

Steps to reproduce

  • confirm that all dependencies are present
$ rpm -qa | egrep "(gcc-c++|glibc-devel|scons|libcurl-devel|gsl-devel|libxml2-devel|zlib-devel|ncurses-devel)"
ncurses-devel-5.7-3.20090208.el6.x86_64
glibc-devel-2.12-1.149.el6_6.5.x86_64
libcurl-devel-7.19.7-40.el6_6.4.x86_64
zlib-devel-1.2.3-29.el6.x86_64
devtoolset-2-gcc-c++-4.8.2-15.el6.x86_64
scons-2.0.1-1.el6.noarch
libxml2-devel-2.7.6-17.el6_6.1.x86_64
gcc-c++-4.4.7-11.el6.x86_64
devtoolset-1.1-gcc-c++-4.7.2-5.el6.x86_64
gsl-devel-1.13-1.el6.x86_64
  • build hpg-variant using scons
$ scons
scons: Reading SConscript files ...

scons: warning: Ignoring missing SConscript 'lib/bioinfo-libs/SConscript'
File "/tmp/hpg-variant-1.0/SConstruct", line 35, in <module>

scons: warning: Ignoring missing SConscript 'lib/common-libs/SConscript'
File "/tmp/hpg-variant-1.0/SConstruct", line 35, in <module>

scons: warning: Ignoring missing SConscript 'lib/math/SConscript'
File "/tmp/hpg-variant-1.0/SConstruct", line 35, in <module>
scons: done reading SConscript files.
scons: Building targets ...
gcc -o src/effect/auxiliary_files_writer.o -c -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -Wuninitialized -Wmissing-braces -O3 -g -I. -Isrc -Iinclude -Ilib/bioinfo-libs -Ilib/common-libs -Ilib/math -I/usr/include -I/usr/local/include -I/usr/include/libxml2 src/effect/auxiliary_files_writer.c
In file included from src/effect/auxiliary_files_writer.c:21:
src/effect/effect_runner.h:44:46: error: bioformats/db/cellbase_connector.h: No such file or directory
src/effect/effect_runner.h:45:56: error: bioformats/features/variant/variant_effect.h: No such file or directory
src/effect/effect_runner.h:46:47: error: bioformats/vcf/vcf_file_structure.h: No such file or directory
src/effect/effect_runner.h:47:37: error: bioformats/vcf/vcf_file.h: No such file or directory
src/effect/effect_runner.h:48:40: error: bioformats/vcf/vcf_filters.h: No such file or directory
src/effect/effect_runner.h:49:38: error: bioformats/vcf/vcf_write.h: No such file or directory
src/effect/effect_runner.h:50:32: error: commons/file_utils.h: No such file or directory
src/effect/effect_runner.h:51:32: error: commons/http_utils.h: No such file or directory
src/effect/effect_runner.h:52:25: error: commons/log.h: No such file or directory
src/effect/effect_runner.h:53:28: error: commons/result.h: No such file or directory
src/effect/effect_runner.h:54:37: error: commons/jansson/jansson.h: No such file or directory
src/effect/effect_runner.h:55:35: error: containers/array_list.h: No such file or directory
src/effect/effect_runner.h:56:29: error: containers/list.h: No such file or directory
src/effect/effect_runner.h:57:41: error: containers/cprops/hashtable.h: No such file or directory
In file included from src/effect/effect_runner.h:59,
                 from src/effect/auxiliary_files_writer.c:21:
src/effect/effect.h:37:40: error: commons/argtable/argtable2.h: No such file or directory
src/effect/effect.h:38:38: error: commons/config/libconfig.h: No such file or directory
In file included from src/effect/effect.h:41,
                 from src/effect/effect_runner.h:59,
                 from src/effect/auxiliary_files_writer.c:21:
src/shared_options.h:36:37: error: bioformats/vcf/vcf_util.h: No such file or directory
In file included from src/effect/effect.h:41,
                 from src/effect/effect_runner.h:59,
                 from src/effect/auxiliary_files_writer.c:21:
src/shared_options.h:109: error: expected specifier-qualifier-list before 'filter_chain'
In file included from src/effect/effect_runner.h:59,
                 from src/effect/auxiliary_files_writer.c:21:
src/effect/effect.h:113: warning: 'struct arg_end' declared inside parameter list
src/effect/effect.h:113: warning: its scope is only this definition or declaration, which is probably not what you want
In file included from src/effect/effect_runner.h:61,
                 from src/effect/auxiliary_files_writer.c:21:
src/hpg_variant_utils.h:28:38: error: bioformats/family/family.h: No such file or directory
src/hpg_variant_utils.h:29:37: error: bioformats/ped/ped_file.h: No such file or directory
src/hpg_variant_utils.h:33:30: error: containers/khash.h: No such file or directory
In file included from src/effect/effect_runner.h:61,
                 from src/effect/auxiliary_files_writer.c:21:
src/hpg_variant_utils.h:46: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
src/hpg_variant_utils.h:49: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
src/hpg_variant_utils.h:56: error: expected declaration specifiers or '...' before 'array_list_t'
src/hpg_variant_utils.h:83: error: expected ')' before '*' token
In file included from src/effect/effect_runner.h:61,
                 from src/effect/auxiliary_files_writer.c:21:
src/hpg_variant_utils.h:85: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
src/hpg_variant_utils.h:88: error: expected ')' before '*' token
In file included from src/effect/auxiliary_files_writer.c:21:
src/effect/effect_runner.h:99: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:100: error: expected declaration specifiers or '...' before 'list_t'
src/effect/effect_runner.h:100: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:100: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:107: error: expected declaration specifiers or '...' before 'cp_hashtable'
In file included from src/effect/auxiliary_files_writer.c:21:
src/effect/effect_runner.h:108: error: expected declaration specifiers or '...' before 'list_t'
src/effect/effect_runner.h:108: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:108: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:110: error: expected declaration specifiers or '...' before 'list_t'
src/effect/effect_runner.h:112: error: expected declaration specifiers or '...' before 'list_t'
src/effect/effect_runner.h:117: error: expected ')' before '*' token
src/effect/effect_runner.h:122: error: expected ')' before '*' token
src/effect/effect_runner.h:128: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:137: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:149: error: expected declaration specifiers or '...' before 'list_t'
src/effect/effect_runner.h:149: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:149: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/effect_runner.h:155: error: expected ')' before '*' token
src/effect/auxiliary_files_writer.c:23: error: expected ')' before '*' token
src/effect/auxiliary_files_writer.c:40: error: expected ')' before '*' token
src/effect/auxiliary_files_writer.c:56: error: expected declaration specifiers or '...' before 'cp_hashtable'
src/effect/auxiliary_files_writer.c: In function 'write_result_file':
src/effect/auxiliary_files_writer.c:58: error: 'result_file_t' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:58: error: (Each undeclared identifier is reported only once
src/effect/auxiliary_files_writer.c:58: error: for each function it appears in.)
src/effect/auxiliary_files_writer.c:58: error: 'result_file' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:68: warning: implicit declaration of function 'result_file_new'
src/effect/auxiliary_files_writer.c:76: error: 'result_item_t' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:76: error: 'meta_item_version' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:76: warning: implicit declaration of function 'result_item_new'
src/effect/auxiliary_files_writer.c:77: error: 'meta_item_date' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:78: error: 'meta_item_tool' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:80: warning: implicit declaration of function 'result_add_meta_item'
src/effect/auxiliary_files_writer.c:93: error: 'input_item_tool' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:94: error: 'input_item_outdir' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:96: error: 'input_item_vcf_file' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:98: error: 'input_item_species' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:102: error: 'input_item_numthreads' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:104: warning: implicit declaration of function 'get_filename_from_path'
src/effect/auxiliary_files_writer.c:105: error: 'input_item_vcf_input' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:107: warning: implicit declaration of function 'result_add_input_item'
src/effect/auxiliary_files_writer.c:113: error: 'output_item' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:121: warning: implicit declaration of function 'result_add_output_item'
src/effect/auxiliary_files_writer.c:122: error: 'shared_options_data_t' has no member named 'chain'
src/effect/auxiliary_files_writer.c:144: warning: implicit declaration of function 'cp_hashtable_get_keys'
src/effect/auxiliary_files_writer.c:144: error: 'summary_count' undeclared (first use in this function)
src/effect/auxiliary_files_writer.c:145: warning: implicit declaration of function 'cp_hashtable_count'
src/effect/auxiliary_files_writer.c:148: warning: implicit declaration of function 'cp_hashtable_get'
src/effect/auxiliary_files_writer.c:183: warning: implicit declaration of function 'result_file_write'
src/effect/auxiliary_files_writer.c:184: warning: implicit declaration of function 'result_file_free'
scons: *** [src/effect/auxiliary_files_writer.o] Error 1
scons: building terminated because of errors.

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