1.0.13

Modified folder structure under alignments for input modes 1,2 and 3.

1.0.12

Release for re-submission.
Modified test scripts and manual.
Added validation and use case tests.

1.0.11

• 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 chararrays 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.

1.0.9

• Bug fixes:
  • There was a problem while running input mode 4, NGS with ART. Some filenames were wrongly formatted.
  • When using also input mode 4, and the replicates had a different number of loci there was a problem in the coverage calculation. Multipliers were using wrong indexes.
  • Job templates and seed files for SGE and SLURM environments have changed. Now the seed files contain all the ART commands, and so the templates simpler.

1.0.8

Bug fixes related to the generation of FASTA files. Specifically with the format of the description.
Also, there are fewer log notifications while iterating over loci for the individual assignment.

1.0.7

This version has been launched with the paper submission to biorxiv.
Several improvements in memory usage and logging messages.

Version 1.0.6

Bug fix related to filtered replicates

1.0.4a0

gene-tree distribution required files paths updated

1.0.4: bug fixes:

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

Version 1.0.3

- Fixed bugs related to runART options.
- Running properly for all test case scenarios.
- Coverage matrix values now formatted to get 3 decimal points (before, 4)
- Some variable names were wrong and therefore raised some errors, this is now fixed.
- When using inputmode=2 (single gene-tree with ancestral sequence) the path of the sequence
was wrongly formatted, now fixed.