comparison news.txt @ 0:061c9e133d1e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty

0:061c9e133d1e

Stacks 2.2 - Aug 22, 2018
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    Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed
             before they are processed.
    Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces 
             --min-kmer-freq which is now deprecated
    Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.

Stacks 2.1 - June 25, 2018
--------------------------
    Bugfix: Fixed a performance regression in sstacks. Recent changes in sstacks made it more likely to
            invoke the gapped algorithm to match to the catalog. In some cases, matches to the catalog
            would be marked as ambiguous alignments and dropped from the next stages of analysis due to 
            differences in CIGAR strings from the gapped alignment. 
    Feature: ustacks Changed --high_cov_thres default value from 2.0 to 3.0.
    Feature: gstacks: Changed --min-kmer-freq default value from 0.05 to 0.01.
    Feature: Added further checks on zlib calls.

Stacks 2.0 - Apr 23, 2018
-------------------------
    Feature: modified cstacks and ustacks gapped alignment algorithms to always align the two stacks/alleles
             with the most k-mers in common, removed the previous minimum k-mer limit.
    Feature: modified cstacks so that when a sample locus matches two or more catalog loci, those catalog
             loci are combined, or rolled-up, reducing undermerged loci that generate excess homozygote calls.
    Feature: modified tsv2bam so that when two loci from the same sample match the same catalog locus, those
             loci are combined.
    Bugfix: corrected BbvCI restriction enzyme to add the missing negative strand sequence.
    Bugfix: corrected the catalog writing routines for unzipped output files to include missing column.
    Bugfix: populations: Fixed the filtering of monomorphic loci.
    Bugfix: populations: Now preserving sample ordering in all outputs.
    Bugfix: Fixed ICPC compilation.

    2.0b - May 1, 2018
    Feature: gstacks: Removed the assertion that the first basepair of each locus should
             be part of a cutsite (now a warning).
    Feature: gstacks: The reported effective coverage is now a more realistic weighted mean.
    Bugfix: populations: Fixed STRUCTURE output being corrupted for some unordereds population maps.

Stacks 2.0 Beta 10 - Apr 10, 2018
---------------------------------
    Feature: Improved gapped alignment for secondary reads in ustacks.
    Feature: Improved populations performance.
    Feature: Added enzymes Cac8I, MslI.
    Feature: Made population maps more tolerant to spurious extra spaces and lines.
    Feature: populations: VCF output: changed the format of the catalog locus field and made the column 1-based.
    Feature: gstacks: increased haplotyping rates by adding a filtering of spurious SNPs step.
    Bugfix:  Fixed populations dramatric slow-down on datasets with more than several hundred samples.
    Bugfix:  Restored the NS/locus distribution in populations's distributions log.
    Bugfix:  Fixed the populations --radpainter export.
    Bugfix:  stacks-dist-extract: Fixed OSX compatibility.
    Bugfix:  Fixed breaking bug in populations --in-vcf mode filtering statistics.

Stacks 2.0 Beta 9 - Mar 12, 2018
--------------------------------
    Feature: Cleaned up tags/snps/alleles/matches files. We removed the batch ID from ustacks and cstacks
             output, and the deprecated log likelihood fields from ustacks and cstacks. We also removed
             the chromosome/bp/strand fields as they are no longer used in these files.
    Feature: Renamed gstacks output files that represent the new components of the catalog:
               gstacks.fa.gz => catalog.fa.gz; gstacks.vcf.gz => catalog.calls
    Feature: Removed read length restrictions from ustacks/cstacks/sstacks core, reads/loci can vary in
             length throughout the pipeline.
    Feature: Reimplemented PLINK export format for the populations program.
    Bugfix: Updated to HTSLib 1.7; changed to a custom build system that will work with the Stacks build
            system.
    Bugfix: Made gapped alignments mandatory in ustacks, cstacks, and sstacks. Added check for frameshift
            at 3' end of the read -- if found, a match is deferred to the gapped aligner.

Stacks 2.0 Beta 8 - Feb 03, 2018
--------------------------------
    Feature: populations: Now calculated deviation from Hardy-Weinberg equilibrium at the SNP level
             (using an exact test), and at the haplotype level (using Guo+Thompson's MCMC algorithm).
    Feature: populations: Added an export type for FineRADStructure.
    Feature: populations: Added the GQ/GL fields in the VCF SNPs output.
    Feature: gstacks: Made the default behavior regarding paired-end reads more logical (in
             reference-based mode --paired has been replaced with --unpaired).
    Feature: gstacks: Added details about samples and coverages to the log outputs.
    Feautre: Added enzymes NspI, BbvCI, fixed BfuCI.
    Bugfix:  corrected a major performance bottleneck in populations when smoothing population statistics
             across the genome.
    Bugfix:  populations: The VCF output now preserves the input sample order.
    Bugfix:  gstacks: Fixed the handling of a rare special case in the PCR duplicates code.
    Bugfix:  gstacks: Fixed 100% being added to all per-thread timings.

Stacks 2.0 Beta 7 - Dec 29, 2017
--------------------------------
    Feature: gstacks: Added an option to remove PCR duplicates based on insert
             size (--rm-pcr-duplicates, plus the related --rm-unpaired-reads).
    Feature: populations: Added a haplotype Genepop export.
    Feature: populations: improved the help; changed the output names for SNP
             files to 'populations.snps.EXT'; added option --no_hap_exports.
    Feature: gstacks and populations: Clarified the logs; moved distributions
             to a separate '.xlog' file and added script stacks-xlog-extract.
    Feature: gstacks: Tweaked the help/interface; especially, replaced --spacer
             with --suffix (for BAM directory input).
    Feature: Added enzymes BfuI and HinP1.
    Feature: Added option --inline_null to clone_filter.
    Bugfix: gstacks: Fixed a typo preventing the paired reads from being merged.
    Bugfix: populations: Fixed a segfault that occurred with some large datasets.
    Bugfix: Made VCF outputs more standard compliant.
    Bugfix: populations: Repaired --fasta_samples and --fasta_samples_raw.
    Bugfix: populations: Fixed population aborting at the end of the run
            when an export option was specified multiple times.
    Bugfix: gstacks: Adjusted progression report for catalog asymmetry.
    Bugfix: Fixed installation of stacks-integrate-alignments on MacOS.

Stacks 2.0 Beta 6 - Dec 02, 2017
--------------------------------
    Feature: Implmented the VCF haplotypes output.
    Bugfix:  Corrected asset failure in populations when exporting data for genepop or structure output.

Stacks 2.0 Beta 5 - Nov 27, 2017
--------------------------------
    Feature: Reimplemented structure, phylip, and phylip_var exports.
    Bugfix: Tightened up the overlap algorithm to require 80% of overlapping sequence to be
            aligned and of the aligned sequence, 80% must be identities.
    Bugfix: Fixed segfault in gstacks when compiled with CLANG on OS X.
    Bugfix: gstacks: Fixed how misphasings are reported.

Stacks 2.0 Beta 4 - Nov 07, 2017
--------------------------------
    Bugfix: Continued improving overlap algorithm to join SE and PE contigs.
    Bugfix: Improved build system to handle new timing functions in gstacks.

Stacks 2.0 Beta 3 - Nov 01, 2017
--------------------------------
    Feature: Added output to populations describing mean PE contig size and mean number of
             genotyped sites per locus, which reflects the current filtering paramters.
    Feature: Improved the output of gstacks and populations.
    Feature: Added script `stacks-integrate-alignments`.
    Bugfix: made further improvements to the single-end/paired-end locus overlapping algorithm.
    Bugfix: fixed all depths being null in populations' VCF output.
    Bugfix: Numerically tweaked the marukilow model to remove a limit case.

Stacks 2.0 Beta 2 - Oct 19, 2017
--------------------------------
    Feature: gstacks: Made it possible to read from multiple BAM files at the same time; modified the
             interface accordingly.
    Feature: gstacks: Parallelized the reference-based mode.
    Feature: gstacks: Added various statistics & improvements to the log output.
    Feature: gstacks: Improved how the forward & paired-end reads are merged (in denovo mode; no more trimming).
    Feature: populations: Added code to calculate the overlap between RAD loci when a reference is available.
    Feature: populations: Added VCF ouput (--vcf).
    Feature: Updated the denovo_map.pl and ref_map.pl wrappers, samples must now be specified using --samples and --popmap.
    Bugfix: Fixed three memory leaks in populations; improved reference-aligned batch logic.
    Bugfix: Improved overlapping code in gstacks to merge more single and paired-end contigs together.
    Bugfix: Now compiles on Apple OS X.
    Bugfix: Fixed a bug that skewed the fixed-site (no-SNP) likelihood in the marukilow model.

Stacks 2.0 Beta 1 - Oct 09, 2017
--------------------------------
    Feature: Paired-end sequencing data can be utilized fully. In particular, when the shearing-based
             protocol is used, the software will assemble a local contig from the paired reads across
             the population, possibly overlap it with the forward-reads region, then align all reads to the
             assembled contig. This new approach also fully supports double-digest protocols.
    Feature: Haplotype calling and diploidy-violation dectection now rely on a novel, more powerful algorithm.
    Feature: SNP and genotype-calling now uses the diploid models of Maruki and Lynch (2017).
    Feature: The rxstacks program has been replaced with the gstacks program, and there is no need to re-run
	     some of the earlier steps of the pipeline anymore.
    Feature: The memory footprint of the populations program has been considerably reduced and can be scaled
	     for any size data set.
    Feature: The reference-based pipeline has been simplified, and now only comprises two steps: gstacks and populations.
    Feature: Added --null_inline mode to clone_filter (and process_radtags) for previously unseen type
             of oligo combination.

Stacks 1.48 - Nov 20, 2017
---------------------------
    Feature: Added HinP1I restriction enzyme.
    Feature: Added --null_inline mode to clone_filter (and process_radtags) for previously unseen type
             of oligo combination.

Stacks 1.47 - Sept 06, 2017
---------------------------
    Feature: Improved populations's fasta output options (especially,
             added a option to export locus consensus sequences).
    Feature: denovo_map.pl and red_map.pl now stop if a component
             of the pipeline fails.
    Feature: Improved the output of denovo_map.pl and ref_map.pl.
    Bugfix: Added a format check in Fasta/GzFasta to avoid a potential
            segfault when working on FastQ files.
    Bugfix: Fixed a bug in count_fixed_catalog_snps.py that could cause
            overwrites when working with uncompressed files.