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File stacks.changes of Package stacks

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Tue Dec  6 14:40:36 UTC 2022 - Pierre Bonamy <flyos@mailoo.org>

- Update to 2.62
Feature: added a '--vcf-all' export to populations which will export fixed
            and variable sites to a VCF file. If '--ordered' is also specified, it
            will only export non-overlapping sites.
Feature: improved ustacks logging to include final number of assembled
            loci; modified denovo_map.pl to include this in its logging output.
            Improved logging in populations program. 
Feature: Added variant of PstI cutsite to process_radtags: pstishi only
            leaves "GCAG" as the cutsite remnant, published in:
        Shirasawa, Hirakawa, and Isobe, 2016, DNA Research; doi: 10.1093/dnares/dsw004 
Bugfix: fixed assert() failure in populations when no population map was
        specified.
Bugfix: updated stacks-dist-extract --pretty print to better handle
        printing comments.
Feature: parallelized process_radtags. Can now run on multiple cores (max of 24 cores), resulting
            in a speedup of 2-3x, depending on physical I/O and number of cores used. Minor improvements
            to output status messages.
Feature: added '--pretty' print option to stacks-dist-extract script.
Bugfix:  corrected bug in parsing of bootstrap archive file, long lines were not properly handled.
Feature: Added HhaI restriction enzyme.
Feature: memory usage reduction in populations. Some examples of memory savings:
    - De novo and Ref-aligned included f-statistic calculations; no filtering employed.
    - Ref-aligned includeds smoothed values.
- 2 populations, 10 samples, 99,505 RAD loci, ~435bp, paired-end reads:
        * Reference-aligned: 2.2Gb vs. 0.9Gb, 59% reduction
        * De novo analysis:  1.5Gb vs. 0.4Gb, 73% reduction
    - 4 populations, 78 samples, 190,912 RAD loci, 94bp, single-end reads:
        * Reference-aligned: 1.8Gb vs. 0.7Gb, 62% reduction
        * De novo analysis:  1.6Gb vs. 0.8Gb, 51% reduction
    - 18 populations, 241 samples, 626,584 RAD loci, ~370bp, paired-end reads:
        * Reference-aligned: 9.3Gb vs. 4.2Gb, 56% reduction
        * De novo analysis: 10.6Gb vs. 6.1Gb, 42% reduction
Feature: re-implemented bootstrapping for smoothed population statistics values calculated in the
            populations program. Bootstrapping is now a two stage process: 1) run populations with the 
            popmap of choice and specify --bootstrap-archive to generate values for resampling. 2) Re-run
            populations with specific boostrap flags (--bootstrap*) to generate p-values for specific
        statistics. Populations will locate bootstrap parchive from previous run to conduct resampling.
Feature: updated gstacks to output a list of chromosomes to 'catalog.chrs.tsv' when processing
            reference-aligned data. These data will then be incorporated by populations into VCF exports allowing
            easier interoperability with vcftools and bcftools.
Feature: simplified SNP-based Fst output files, discarded some outputs rarely used for memory savings. Reduced
            significant digits of some outputs (log-odds and confidence intervals) to save internal memory.
Bugfix:  There was a small regression in clone_filter causing it to mishandle --null-index style oligos.
Bugfix:  loci could be presented out of order in populations.snps.vcf and populations.haps.vcf when they
            originated from consecutive scaffolds with single loci on each. This prevented bcftools and other
            programs from properly indexing the VCF files.
Bugfix:  populations.phistats.tsv had last line truncated due to file not being closed properly.
Bugfix:  instituted maximum thread count for component programs.
Feature: updated populations to output the number of missing sites and loci, per sample to the
            populations.log.distribs file.
Feature: replaced stacks-integrate-alignments with a new Python program. This new program allows for greater
            filtering of alignments and more error checking for alignments where an fragment alignment could
            associate SNPs within loci that had non-existent coordinates (on the reference genome).
Feature: updated populations to look for and if found, load the file 'catalog.chrs.tsv' in the Stacks output
            directory. This is then exported as part of the VCF headers to supply contig names/lengths.
Feature: updated the process_radtags log file to have similar headers to the *.distribs files and the ability
            to extract portions of the log with stacks-dist-extract utility.
Feature: updated denovo_map.pl to print more data to logfile for ustacks executions, including max depth,
            number and percent of reads incorporated. Made output compatible with stacks-dist-extract utility.
Feature: updated denovo_map.pl and ref_map.pl to print more detailed message upon failure, including last
            command executed.
Bugfix:  In the populations program, the phylip-all export would throw an error (or misprint the sequences)
            if the population names were of different lengths.
Bugfix: Fixed several memory errors in ustacks related to processing trimmed reads.
Feature: updated process_radtags so that if you specify the same sample name in the barcodes file for multiple
            barcodes, the program will merge the output for those barcodes into the single, specified output file.
Feature: changed the default 'smoothed' and 'bootstrap' values in output files to contain a -1.0 if a particular locus
            was not included in the smoothing/bootstrap algorithms (this occurs when RAD loci overlap the same genomic
            region and only one of the loci can be included in the smoothing/bootstrapping).
Bugfix: Reverted earlier changes to ensure all mentions of column position (within a RAD locus) are zero-based, while
        reference-based coordinates are one-based.
Bugfix: Updated populations VCF export so that snp_cols variable (tells you where the individual SNPs come from for a
    set of haplotypes is in the proper order when the locus is on the negative strand (we reversed the order here).
Bugfix: Corrected process_radtags when processing dual index barcodes but only the second, i7 barcode is an actual
        barcode, referred to as --null_index in the process_radtags barcodes options. In these cases, the first, i5
        index barcode is being used as a random oligo to remove PCR duplicates.
Feature: Added NgoMIV restriction enzyme to process_radtags.
Feature: Added GTF export to populations, for reference-aligned data.
Feature: Added BtgI, PacI, and PspXI, HpyCH4IV restriction enzymes to process_radtags.
Bugfix: stacks-integrate-alignments, tab characters fed to the grep were not being interpreted properly
Bugfix: denovo_map.pl was broken for running cstacks on non-genetic map datasets.
Feature: denovo_map.pl now has a --resume options, which will restart the pipeline if a previous run failed
        to complete.
Bugfix: Improved denovo_map.pl wrapper so that if a genetic map is specified in the population map, only samples
        labeled 'parent' are loaded into the catalog during the cstacks stage.
Bugfix: corrected malfunctioning error message in populations when improper population names supplied for genetic map.
Bugfix: populations VCF export: changed the ID field (for denovo), paritally reverting it back to v1 format. The first
        three colums, 'chr  basebapir  ID' are now represented in the de novo format as 'cloc  col1  cloc:col1',
        where cloc is the catalog locus number, col1 is the 1-based position of the SNP within the locus and the ID field is a
    concatenation of the two (making each SNP have an ID that is a combination of lucus ID and column).
Bugfix: Change the Phylip-var-all export from populations to insert a tab after the sample name, instead of padding with space.
Feature: genotyping for mapping crosses has been (re)added to the populations program. (In Stacks v1, this was done by
            the now deprecated genotypes program. Mapping genotypes can be exported for JoinMap, r/QTL, or OneMap by
            specifying the --map-type and --map-format options (with a parent/progeny population map) to populations.
Feature: gstacks: catalog.fa.gz files are now directly indexable.
Bugfix:  denovo_map.pl: added code to properly handle '.1' suffix on input files without having to modify the population map.
Bugfix:  gstacks: fixed target indexes being shifted in the BAM files produced by --write-alignments.
Bugfix:  gstacks: fixed --write-alignments not respecting -O.
Bugfix:  populations: fixed polyallelic SNPs causing an abort near PopSum.cc:96 (cf. marukihigh model & external VCFs).
Feature: populations: calculates haplotype-based Dxy (Nei, 1987) and provides for smoothing if a 
            reference genome is available.
Feature: populations: re-implemented full sequence export for phylip format, including partitioning information.
Feature: populations: re-implemented HZAR export.
Feature: added reporting code to detect issues with inconsistent versions of libz on a host system
            causing Stacks components to fail to open compressed files.
Feature: gstacks: improved PCR duplicate reporting to be per-sample.
Bugfix:  populations: fixed an issues where the basepair position of a small number of loci was reported
                        incorrectly -- they were shifted by a small, fixed offset.
Feature: populations: Backwards-compatibly worked on filtering options; added long names for -r and -p and
            added --min-samples-overall and --filter-haplotype-wise.
Feature: populations: Implemented --treemix.
Feature: gstacks: Improved RAD-loci reference sequences around the end of forward (restriction site-bound) reads.
Feature: gstacks: Improved the way 2-microsatelittes are dealt with.
Feature: gstacks: Changed the default value for --var-alpha from 0.05 to 0.01 (--gt-alpha is unchanged at 0.05).
Feature: gstacks: Improved PCR duplicates-related log information (distribution of clone sizes).
Feature: gstacks: Added an option to save read alignments (--write-alignments).
Feature: Backwards-compatibly switched to hyphens in command line options (underscores remain accepted
            where they previously were).
Feature: cstacks/sstacks now report an error when the disk becomes full.
Bugfix: Fixed some limit cases causing an abort at gstacks.cc:1752.
Bugfix: Fixed some limit cases causing an abort at debruijn.cc:60.
Bugfix: Fixed some limit cases apparently causing an infinite loop in the de Bruijn code.
Bugfix: Restored compilation with the oldest C++11 GCC versions (4.9 and 5.0).
Bugfix: Fixed assert failure at gstacks.cc:1171 (corrected with a return on gstacks.cc:1126)
Bugfix: inadvertantly compiling out BAM support from process_radtags due to the removal of the HAVE_BAM
            config option, which occurred when we moved the BAM library internally to Stacks.
Bugfix: corrected infinite loop in populations when --write-single-snp and -r were enabled.
    Bugfix: correct missing comment marker in population's FASTA exports and missing ']' character in FASTA comments.
Bugfix: the snps_per_loc_postfilters distribution in the populations.log.distrib file was slightly off due to counting
            the number of SNPs at loci where despite SNP objects present at the locus, all sites were fixed in the
        focal populations.
Bugfix: Some haplotypes could pass through the filter, even after particular SNPs were filtered from them.
Bufgix: Corrected the samples per locus and absent-samples per locus distributions from populations. 
Bugfix: the --write-random-snp flag was causing an infinite loop in populations.
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: Fixed a breaking circumstantial segmentation fault in populations
Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.

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Thu Jul 12 10:57:41 UTC 2018 - flyos@mailoo.org

- Update to 2.1
- Fixed issue with shebang in perl and python files
- Cleaned spec file using spec-cleaner

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Fri Jan 20 00:17:23 UTC 2017 - flyos@mailoo.org

- Update to 1.44
- Enabled SparseHash feature
- Clean samtools dependency

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Sat Apr 30 16:25:54 UTC 2016 - flyos@mailoo.org

- Cleaner spec file

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Thu Apr 21 15:06:46 UTC 2016 - flyos@mailoo.org

- Changed "./configure" and "make install" for "%configure" and "%make_install"

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Wed Apr 20 19:04:22 UTC 2016 - flyos@mailoo.org

Initial release.-

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