minor update

1-4-1a

forgot requirement for numpy

1-4-1

Merge pull request #40 from andersgs/fix_setup

Fix typo in setup.py causing it to silently fail installation

1-4

Rewrite of vcf2fasta, additional parameters, significant speed-up for higher numbers for vcf files

Version 1-3

Merge pull request #33 from aunderwo/master

correct max vcf size finding

Minor Bug Fixes

Bugs fixed:

• #23, #24 - Version and all scripts are now properly accessible from command line.
• Stats and alignments recalculated after removing samples/columns with fractions of N and gaps above given threshold.
• Cool, naive recombination removal, thanks @ulfschaefer
• Other minor bug and doc fixes.

Optimisations

We have looked into the memory consumption of some of the processes and optimised them. vcf2fasta can run locally for many many VCFs without running out of memory and crashing. filter_vcf runtime has also been improved, along with memory utilisation.

• Memory optimisations: #12
• Annotating variants is also optimised to use only the momery required.
• Fixed issue with N in the reference where we have to insert it for mpileup to work., #13.
• samtools sort is supplied with -m option if there is at least 1G of memory per CPU. When there is enough memory, sort will be done in-memory, instead of temp files.
• --with-mixtures option allows to output IUPAC extended alphabet mixture codes, for SNP positions that FAIL filters, based on frequency threshold. E.g. if threshold is set to 0.2, and record is A:50,T:50 for REF and ALT, then both are used because for each base mixture is 0.5. However, if A:2, T:98, then only T is used because A's ratio is 0.02. Multi ALT bases are also treated in the same fashion.
• Progress for vcf2fasta based on guestimate of total number of records
• Bug fixes

Minor Release

A critical error snuck into previous release, multi-contig/chromosome mapping was not done prperly and most of the variants were discarded. This release fixes the issue.

Version 1 of the PHEnix pipeline.

Pipeline can be accessed using

phenix.py [--debug] run_snp_pipeline --help

option. Additional commands can be found in the documentation on http://phenix.readthedocs.io/en/latest/.