First stable release

First stable release! Comments and feedback are welcome!

Not many changes since the last release candidate, many of them oriented to improve usability:

• 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

Great performance improvements and full support for VCF v4.1

Great reduction of memory usage in the VCF merging tool allows to merge hundreds of VCF files at twice the previous speed

Full support for Variant Call Format v4.1, including structural variants and novel adjacencies with breakends

Command-line autocompletion in Bash shell

SNP ID shown in GWAS output report

New statistics per group and usability improved

VCF stats: Statistics can be calculated using any column in the PED as grouping criteria, so not only case-control grouping can be performed, but also by sex, population, and so on

VCF merge:

• It no longer gets blocked when only one file pending
• Removes duplicates from the FILTER column

New command-line options: --version, --log-level

Parallelism configuration made easier by removing the "entries-per-thread" option (now calculated automatically)

Better handling of multi-allelic variants

VCF merging tool more tolerant to different reference alleles (can be configured via the –strict-ref argument)

hpg-var-effect checks all alternate alleles of a single variant

Memory leaks in hpg-var-effect supressed

VCF tools vastly improved, much faster VCF merge

VCF filter

• New filters by gene, region+type, being or not an indel, and inheritance pattern (dominant/recessive)
• Great performance improvement in single-core upto 2x
• Multi-threaded implementation
• GFF/BED as input for region filtering

VCF statistics

• New statistics about mendelian errors per sample, being or not an indel, inheritance pattern per variant
• Saving result statistics to SQLite DB file

VCF merge: Great reduction of memory usage, performance improvement upto 3x

VCF split: By coverage intervals

Bug solved: Accept VCF files with arbitrary header length

Miscellaneous: Some library dependencies packaged inside the application

Usability improvements

Filter output uses default names (your_vcf_file.vcf.filtered and your_vcf_file.vcf.rejected), –out argument reserved for tool output

Merge tool notifies when a sample appears more than once

GWAS analysis notify when a sample appears more than once

GWAS analysis improved (again!)

GWAS analysis: Properly manage individuals with no ancestors nor sex specified

GWAS analysis improved

GWAS analysis: Properly process PED files with no family structure, and VCF files with less samples than the PED file

Filter of VCF files by percentage of missing values

Effect tool tries to reconnect when an error occurs

Effect tool tries to reconnect 3 times when an error occurs. VCF records still not processed are written to a file.

New VCF tools included

Split in multiple binaries: hpg-var-effect, hpg-var-gwas, hpg-var-vcf

Sorting results of GWAS tests

Tools for preprocessing Variant Call Format (VCF) files:

• Merge multiple files
• Filter by minimum allele frequency (MAF)
• Configuring whether to write to file the VCF records rejected by a filter

SCons used as build system instead of Make