Ngsphy

- Added: now printing a summary log with the importat parameters of the simulation.
- Added: random seed option in the general block.
- Added: the general random seed allows to automatically set up the indelible's control random seed when using inputmode in [1,2,3].
- Added: use cases for variant recovery and tree inference.
- Added: for input mode 2 and 3, where a sequence (anchor or ancestral) is introduced, there's a base frequency calculation to input into indelible, in case it is not explicit in the indelible-ngsphy control file.
- Update: on re-rooting. Now the tree is re-rooted on a dichotomy, with the outgroup branch length 0.
- Update: on NGS mode == readcounts, the output VCF file, renaming the ID for each record of the file.
- Update: now NGSphy produces folder with more descriptive names.
- Update: now possible to decide within [ngs-reads-art] options, whether coverage is per amplicon (fcov) or the total number of reads (rcount).
- Fixed: coverage calculation for diploid individuals updated.
- Fixed: coverage distribution parameterization.
- Fixed: a bug related to coverage computations. The indexes are now within the ranges.
- Fixed: a bug which modified the sequences generated from INDELible with the anchor sequence. This resulted in adding the wrong line
of the anchor file to the sequence dictionary, altering the resulting individual and generating a void FASTQ file.
- Fixed: (read counts) There was a problem in the output VCF file for read counts. Header was incorrect and CHROM id was related to the replicate/locus info and not to the name (description) of the reference sequence. File runs properly in tools like `vcftools` and CHROM field is now the description of the reference allele sequence.
- Fixed: (read counts) There was not an initialization in some NumPy `chararray`s and this was generating weird symbols, which didn't properly generate the data that was written
down in the VCF files. This was a particular situation for `ploidy == 2`. This has now been fixed.

- trying to fix the gene-tree distribution input mode. Basepath was not being assigned.

bug fixes:
- while using gene-tree distributions, output and input folders where mixed and readings were being made incorrectly. Now fixed.

bug fixes:
- runART option was not retrieved from the settings, so automatically it was not running ART. now fixed.
- runs correctly now for input mode 4.
- coverage matrix floating points now 3 (before 4)
- when handling ancestral sequence file, the access to the sequence was wrong.
- some variable names were misspelled.

bug fixes:
- checking existence of INDELible control file: path generated was badly formatted.
- checking branch lengths of the trees now works fine.
- the streams to check the dependencies of the third-party software now work fine.
- for the sequence generation, I was using a wrong variable name for settings, now works fine
- dendropy depency was missing in some files
- removed the extra folder generated in alignments
- error writing VCF files, all files were written in the no_error folder. fixed.

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