diff --git a/README b/README index fa6e6c7..62454cd 100644 --- a/README +++ b/README @@ -8,7 +8,7 @@ It uses parallel computing technologies such as OpenMP in order to reduce the pr It contains three binaries: * hpg-var-effect retrieves the effect of genome variations. * hpg-var-gwas conducts genomic-wide association analysis such as chi-square and Fisher's exact test, and family-based analysis such as transmission disequilibrium test (TDT)., -* hpg-var-vcf allows one to preprocess files containing genome variations in Variant Call Format. +* hpg-var-vcf allows to preprocess files containing genome variations in Variant Call Format. Filtering, merging, splitting and retrieving statistics are the features currently implemented. CONTENTS diff --git a/SConstruct b/SConstruct index b6a23a5..7fde468 100644 --- a/SConstruct +++ b/SConstruct @@ -51,7 +51,7 @@ t = SConscript("test/SConscript", exports = ['env', 'debug', 'commons_path', 'bi # For the packaging manager: Don't forget to point the XXX_INCLUDE_PATH and XXX_LIBRARY_PATH # variables to the application libraries folder!! tb = env.Package(NAME = 'hpg-variant', - VERSION = '0.99.4', + VERSION = '1.0', PACKAGEVERSION = 0, PACKAGETYPE = 'src_targz', source = env.FindSourceFiles() + env.FindHeaderFiles(progs) + diff --git a/deb/SConscript b/deb/SConscript index b314af4..dca2907 100644 --- a/deb/SConscript +++ b/deb/SConscript @@ -4,7 +4,7 @@ Import('env') # exported by parent SConstruct # Here's the core info for the DEBIAN/control file of the package DEBNAME = "hpg-variant" -DEBVERSION = "0.99.4" +DEBVERSION = "1.0" DEBMAINT = "Cristina Yenyxe Gonzalez Garcia " DEBARCH = "amd64" DEBDEPENDS = "libc6, libcurl4-openssl-dev, libgsl0ldbl, libxml2, zlib1g" @@ -18,8 +18,9 @@ DEBDESC = ''.join([ "Bioinformatics tool suite for analyzing genomic variations\ " * hpg-var-gwas conducts genomic-wide association analysis such as chi-square\n", " and Fisher's exact test, and family-based analysis such as transmission\n", " disequilibrium test (TDT).\n", -" * hpg-var-vcf allows one to preprocess files containing genome variations in\n", -" Variant Call Format." ]) +" * hpg-var-vcf allows to preprocess files containing genome variations in\n", +" Variant Call Format. Filtering, merging, splitting and retrieving \n" +" statistics are the features currently implemented." ]) DEBFILES = [ # Now we specify the files to be included in the .deb diff --git a/rpm/SConscript b/rpm/SConscript index 3ee7d86..74853bb 100644 --- a/rpm/SConscript +++ b/rpm/SConscript @@ -3,14 +3,14 @@ import hashlib, os, shutil, sys Import('env') # exported by parent SConstruct RPMNAME = "hpg-variant" -RPMVERSION = "0.99.4" +RPMVERSION = "1.0" RPMARCH = "x86_64" RPMBUILDREQUIRES = "gcc glibc-devel scons libcurl-devel gsl-devel libxml2-devel ncurses-devel zlib-devel".split(" ") RPMREQUIRES = "libcurl gsl libxml2 zlib".split(" ") # what are we dependent on? -RPMSUMMARY = "HPG Variant summary" +RPMSUMMARY = "HPG Variant is a suite for the study of genomic variations" RPMDESC = "HPG Variant retrieves the effect of genome mutations and allows to conduct analysis" RPMSECTION = "Application/Engineering" -RPMSOURCE = "hpg-variant-0.99.4.tar.gz" +RPMSOURCE = "hpg-variant-1.0.tar.gz" RPMURL = "http://bioinfo.cipf.es" RPMBUILDIR = 'rpmbuild' diff --git a/rpm/hpg-variant.spec b/rpm/hpg-variant.spec index 7bcc7cd..0167ac2 100644 --- a/rpm/hpg-variant.spec +++ b/rpm/hpg-variant.spec @@ -1,5 +1,5 @@ %define name hpg-variant -%define version 0.99.4 +%define version 1.0 Name: %{name} Version: %{version} Release: 1%{?dist} @@ -32,8 +32,9 @@ It contains three binaries: * hpg-var-gwas conducts genomic-wide association analysis such as chi-square and Fisher's exact test, and family-based analysis such as transmission disequilibrium test (TDT). -* hpg-var-vcf allows one to preprocess files containing genome variations in - Variant Call Format. +* hpg-var-vcf allows to preprocess files containing genome variations in + Variant Call Format. Filtering, merging, splitting and retrieving statistics + are the features currently implemented. %prep %setup -q @@ -68,6 +69,13 @@ cp bin/bash_completion/hpg-var-vcf %{buildroot}%{_sysconfdir}/bash_completion.d/ %changelog +* Thu Nov 07 2013 Cristina Yenyxe Gonzalez - 1.0 +- Support for multigenerational families in PED files +- Merge tool notifies when files are unsorted +- All tools notify when output files can't be created +- Sample statistics added to database generated by hpg-var-vcf stats +- Logging output redirection: DEBUG/INFO to stdout, WARN/ERROR/FATAL to stderr + * Wed Sep 18 2013 Cristina Yenyxe Gonzalez - 0.99.4 - Great reduction of memory usage in the VCF merging tool allows to merge hundreds of VCF files at twice the previous speed diff --git a/src/hpg_variant_utils.c b/src/hpg_variant_utils.c index 8f21b10..a36c1e5 100644 --- a/src/hpg_variant_utils.c +++ b/src/hpg_variant_utils.c @@ -321,7 +321,7 @@ void show_usage(char *tool, void **argtable) { } void show_version(char *tool) { - printf("HPG Variant %s %s\nCopyright (C) 2013 Institute for Computational Medicine (CIPF).\n\ + printf("HPG Variant %s %s\nCopyright (C) 2012-2013 Institute for Computational Medicine (CIPF).\n\ This is free software; see the source for copying conditions.\n", tool, HPG_VARIANT_VERSION); } diff --git a/src/hpg_variant_utils.h b/src/hpg_variant_utils.h index d90b3eb..9e6cafa 100644 --- a/src/hpg_variant_utils.h +++ b/src/hpg_variant_utils.h @@ -35,7 +35,7 @@ #include "shared_options.h" -#define HPG_VARIANT_VERSION "0.99.4" +#define HPG_VARIANT_VERSION "1.0" /* *********************** * Initialization *