Redundans

- preprocessing
- more accurate libs stats estimation (using 5% of the genome in the longest contigs)
- reduction:
- improved speed and accuracy
- scaffolding:
- using combination of snap+lastal - very fast and super sensitive!
- no gap closing during scaffolding?

TBD
- check if something need recompilation and try to recompile
- instead of processing 100M reads for 4 libs with similar IS, split it by 25M each
- bioconda
- speed-up gap closing - so far the slowest step! (5/7 of the run!)

- reduction:
- improved sensitivity of reduciton (local alignment mode)
- no need for assembly sorting
- scaffolding:
- bwa mem is way more sensitive, so it's used by default instead of snap

- added long reads (**EXPERIMENTAL**) & reference-based scaffolding support (through [pyScaf](https://github.com/lpryszcz/pyScaf))
- added all dependencies to github
- INSTALL.sh downloads & compiles everything
- all necessary paths are defined by `redundans.py`
- README.md updated
- docs/README.md reduce and updated
- contigs FastA is sorted by descending contig size & contigs below `--minLength` are removed (this speeds up reduction greatly)
- code was polished & optimised, especially in reduction step (`fasta2homozygous.py`)
- subprocess is closed when not needed to lower memory footprint
- speed-optimised: avoided LASTal results sorting by sorting input (contigs FastA)
- memory-optimised ie. generator instead of list (thanks to sorted contigs FastA) (RAM usage: 150G -> 1G)
- contigs FastA file has to be ordered by descending contig size!
- prints how many iterations in total ie. `iteration 1.1 of 2.2 ...`
- libraries stats are estimated after reduction (avoiding double estimations for crappy libs)
- insert size estimated only on the major read orientation
- reduction:
- plotting identity histogram of heterozygous contigs as `contigs.reduced.fa.hist.png`
- reporting heterozygous contigs statistics in `contigs.reduced.fa.hetero.tsv`
- scaffolding:
- added [SNAP aligner](https://github.com/amplab/snap), faster mapping alternative to BWA MEM

- added `--resume` option
- added warning if unable to fetch dependencies versions
- reduction step `fasta2homozygous.py`
- produce more accurate identity between recognised heterozygous contigs
- polished code

- LASTal version checked on runtime
- added FastaIndex.py
- generate stats into .fai file - `samtools faidx` compatible
- simplified dependencies
- Biopython, scipy, numpy & SQLite no longer needed

- improved reduction step performance (fasta2homozygous.py)
- no sorting - greatly improves performance on large and fragmented genomes
- removed `-S / --sortopt` parameter
- no BLAT - unable to multi-thread BLAT, thus relying on LAST completely
- global alignment `-T 1`, instead of local - speed-up and less permissive (more accurate) reduction
- enabled [multi-threading in LAST from v693](http://last.cbrc.jp/last/index.cgi/rev/4174fdbdb9a1)
- no temp files
- all is processed through pipes
- removed unnecessary maf-convert, gzip and file parsing
- code polished