Some routine changes and parser fixes

Changes

• Moved ScanDatabase functions to vdjdb, no longer depends on vdjdb during compilation
• Add unweighted option to downsampling
• Add SelectTop routine

Fixes

• Fix immunoseq parser, the "deduced" CDR3 amino acids issue
• Fix for IMGT parser
• Fix for sample output

1.0.3

Version update

Some updates and fixes

Updates:

• Changed default settings for CalcCdrAAProfile
• Alternative (better) plotting for paired sample intersection stack area plot
• Added simple parser for ImSEQ software (https://github.com/lkuchenb/imseq)

Fixes:

• Correct frequency calculation for software that provides only by-read output (e.g. IMGT)
• Fixed bug in plotting Venn diagrams for 4 and 5 samples

CDR3 amino acid composition

Features added:

• CDR3 amino acid composition profiles that use physical features of amino acid, see related docs

Bug fixes:

• Empty metadata column fix
• milib stop codon character (_) not properly parsed in some formats

Other:

• Make sure you are using JRE v1.8 (you can still build this software under JRE v1.7 from source)
• Improved documentation

First release

Features added:

• Png graphics export
• Insert size table
• Support for MiXCR input
• Optimization for CDR3 sequence and segment storage, ~2x lower memory usage

Bug fixes:

• Segment usage crash on a sample collection with a single empty sample
• Pool samples not flushing output stream
• Join samples crashing on Vienn diagram plot
• Minor fixes for parsers

Snapshot release

1.0-SNAPSHOT

Some code grooming