174 lines
13 KiB
Plaintext
174 lines
13 KiB
Plaintext
-------------------------------------------------------------------
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Tue Dec 6 14:40:36 UTC 2022 - Pierre Bonamy <flyos@mailoo.org>
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- Update to 2.62
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Feature: added a '--vcf-all' export to populations which will export fixed
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and variable sites to a VCF file. If '--ordered' is also specified, it
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will only export non-overlapping sites.
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Feature: improved ustacks logging to include final number of assembled
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loci; modified denovo_map.pl to include this in its logging output.
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Improved logging in populations program.
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Feature: Added variant of PstI cutsite to process_radtags: pstishi only
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leaves "GCAG" as the cutsite remnant, published in:
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Shirasawa, Hirakawa, and Isobe, 2016, DNA Research; doi: 10.1093/dnares/dsw004
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Bugfix: fixed assert() failure in populations when no population map was
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specified.
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Bugfix: updated stacks-dist-extract --pretty print to better handle
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printing comments.
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Feature: parallelized process_radtags. Can now run on multiple cores (max of 24 cores), resulting
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in a speedup of 2-3x, depending on physical I/O and number of cores used. Minor improvements
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to output status messages.
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Feature: added '--pretty' print option to stacks-dist-extract script.
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Bugfix: corrected bug in parsing of bootstrap archive file, long lines were not properly handled.
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Feature: Added HhaI restriction enzyme.
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Feature: memory usage reduction in populations. Some examples of memory savings:
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- De novo and Ref-aligned included f-statistic calculations; no filtering employed.
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- Ref-aligned includeds smoothed values.
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- 2 populations, 10 samples, 99,505 RAD loci, ~435bp, paired-end reads:
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* Reference-aligned: 2.2Gb vs. 0.9Gb, 59% reduction
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* De novo analysis: 1.5Gb vs. 0.4Gb, 73% reduction
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- 4 populations, 78 samples, 190,912 RAD loci, 94bp, single-end reads:
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* Reference-aligned: 1.8Gb vs. 0.7Gb, 62% reduction
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* De novo analysis: 1.6Gb vs. 0.8Gb, 51% reduction
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- 18 populations, 241 samples, 626,584 RAD loci, ~370bp, paired-end reads:
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* Reference-aligned: 9.3Gb vs. 4.2Gb, 56% reduction
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* De novo analysis: 10.6Gb vs. 6.1Gb, 42% reduction
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Feature: re-implemented bootstrapping for smoothed population statistics values calculated in the
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populations program. Bootstrapping is now a two stage process: 1) run populations with the
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popmap of choice and specify --bootstrap-archive to generate values for resampling. 2) Re-run
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populations with specific boostrap flags (--bootstrap*) to generate p-values for specific
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statistics. Populations will locate bootstrap parchive from previous run to conduct resampling.
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Feature: updated gstacks to output a list of chromosomes to 'catalog.chrs.tsv' when processing
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reference-aligned data. These data will then be incorporated by populations into VCF exports allowing
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easier interoperability with vcftools and bcftools.
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Feature: simplified SNP-based Fst output files, discarded some outputs rarely used for memory savings. Reduced
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significant digits of some outputs (log-odds and confidence intervals) to save internal memory.
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Bugfix: There was a small regression in clone_filter causing it to mishandle --null-index style oligos.
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Bugfix: loci could be presented out of order in populations.snps.vcf and populations.haps.vcf when they
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originated from consecutive scaffolds with single loci on each. This prevented bcftools and other
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programs from properly indexing the VCF files.
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Bugfix: populations.phistats.tsv had last line truncated due to file not being closed properly.
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Bugfix: instituted maximum thread count for component programs.
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Feature: updated populations to output the number of missing sites and loci, per sample to the
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populations.log.distribs file.
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Feature: replaced stacks-integrate-alignments with a new Python program. This new program allows for greater
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filtering of alignments and more error checking for alignments where an fragment alignment could
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associate SNPs within loci that had non-existent coordinates (on the reference genome).
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Feature: updated populations to look for and if found, load the file 'catalog.chrs.tsv' in the Stacks output
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directory. This is then exported as part of the VCF headers to supply contig names/lengths.
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Feature: updated the process_radtags log file to have similar headers to the *.distribs files and the ability
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to extract portions of the log with stacks-dist-extract utility.
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Feature: updated denovo_map.pl to print more data to logfile for ustacks executions, including max depth,
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number and percent of reads incorporated. Made output compatible with stacks-dist-extract utility.
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Feature: updated denovo_map.pl and ref_map.pl to print more detailed message upon failure, including last
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command executed.
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Bugfix: In the populations program, the phylip-all export would throw an error (or misprint the sequences)
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if the population names were of different lengths.
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Bugfix: Fixed several memory errors in ustacks related to processing trimmed reads.
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Feature: updated process_radtags so that if you specify the same sample name in the barcodes file for multiple
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barcodes, the program will merge the output for those barcodes into the single, specified output file.
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Feature: changed the default 'smoothed' and 'bootstrap' values in output files to contain a -1.0 if a particular locus
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was not included in the smoothing/bootstrap algorithms (this occurs when RAD loci overlap the same genomic
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region and only one of the loci can be included in the smoothing/bootstrapping).
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Bugfix: Reverted earlier changes to ensure all mentions of column position (within a RAD locus) are zero-based, while
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reference-based coordinates are one-based.
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Bugfix: Updated populations VCF export so that snp_cols variable (tells you where the individual SNPs come from for a
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set of haplotypes is in the proper order when the locus is on the negative strand (we reversed the order here).
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Bugfix: Corrected process_radtags when processing dual index barcodes but only the second, i7 barcode is an actual
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barcode, referred to as --null_index in the process_radtags barcodes options. In these cases, the first, i5
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index barcode is being used as a random oligo to remove PCR duplicates.
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Feature: Added NgoMIV restriction enzyme to process_radtags.
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Feature: Added GTF export to populations, for reference-aligned data.
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Feature: Added BtgI, PacI, and PspXI, HpyCH4IV restriction enzymes to process_radtags.
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Bugfix: stacks-integrate-alignments, tab characters fed to the grep were not being interpreted properly
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Bugfix: denovo_map.pl was broken for running cstacks on non-genetic map datasets.
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Feature: denovo_map.pl now has a --resume options, which will restart the pipeline if a previous run failed
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to complete.
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Bugfix: Improved denovo_map.pl wrapper so that if a genetic map is specified in the population map, only samples
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labeled 'parent' are loaded into the catalog during the cstacks stage.
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Bugfix: corrected malfunctioning error message in populations when improper population names supplied for genetic map.
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Bugfix: populations VCF export: changed the ID field (for denovo), paritally reverting it back to v1 format. The first
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three colums, 'chr basebapir ID' are now represented in the de novo format as 'cloc col1 cloc:col1',
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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
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concatenation of the two (making each SNP have an ID that is a combination of lucus ID and column).
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Bugfix: Change the Phylip-var-all export from populations to insert a tab after the sample name, instead of padding with space.
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Feature: genotyping for mapping crosses has been (re)added to the populations program. (In Stacks v1, this was done by
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the now deprecated genotypes program. Mapping genotypes can be exported for JoinMap, r/QTL, or OneMap by
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specifying the --map-type and --map-format options (with a parent/progeny population map) to populations.
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Feature: gstacks: catalog.fa.gz files are now directly indexable.
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Bugfix: denovo_map.pl: added code to properly handle '.1' suffix on input files without having to modify the population map.
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Bugfix: gstacks: fixed target indexes being shifted in the BAM files produced by --write-alignments.
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Bugfix: gstacks: fixed --write-alignments not respecting -O.
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Bugfix: populations: fixed polyallelic SNPs causing an abort near PopSum.cc:96 (cf. marukihigh model & external VCFs).
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Feature: populations: calculates haplotype-based Dxy (Nei, 1987) and provides for smoothing if a
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reference genome is available.
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Feature: populations: re-implemented full sequence export for phylip format, including partitioning information.
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Feature: populations: re-implemented HZAR export.
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Feature: added reporting code to detect issues with inconsistent versions of libz on a host system
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causing Stacks components to fail to open compressed files.
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Feature: gstacks: improved PCR duplicate reporting to be per-sample.
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Bugfix: populations: fixed an issues where the basepair position of a small number of loci was reported
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incorrectly -- they were shifted by a small, fixed offset.
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Feature: populations: Backwards-compatibly worked on filtering options; added long names for -r and -p and
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added --min-samples-overall and --filter-haplotype-wise.
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Feature: populations: Implemented --treemix.
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Feature: gstacks: Improved RAD-loci reference sequences around the end of forward (restriction site-bound) reads.
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Feature: gstacks: Improved the way 2-microsatelittes are dealt with.
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Feature: gstacks: Changed the default value for --var-alpha from 0.05 to 0.01 (--gt-alpha is unchanged at 0.05).
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Feature: gstacks: Improved PCR duplicates-related log information (distribution of clone sizes).
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Feature: gstacks: Added an option to save read alignments (--write-alignments).
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Feature: Backwards-compatibly switched to hyphens in command line options (underscores remain accepted
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where they previously were).
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Feature: cstacks/sstacks now report an error when the disk becomes full.
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Bugfix: Fixed some limit cases causing an abort at gstacks.cc:1752.
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Bugfix: Fixed some limit cases causing an abort at debruijn.cc:60.
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Bugfix: Fixed some limit cases apparently causing an infinite loop in the de Bruijn code.
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Bugfix: Restored compilation with the oldest C++11 GCC versions (4.9 and 5.0).
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Bugfix: Fixed assert failure at gstacks.cc:1171 (corrected with a return on gstacks.cc:1126)
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Bugfix: inadvertantly compiling out BAM support from process_radtags due to the removal of the HAVE_BAM
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config option, which occurred when we moved the BAM library internally to Stacks.
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Bugfix: corrected infinite loop in populations when --write-single-snp and -r were enabled.
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Bugfix: correct missing comment marker in population's FASTA exports and missing ']' character in FASTA comments.
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Bugfix: the snps_per_loc_postfilters distribution in the populations.log.distrib file was slightly off due to counting
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the number of SNPs at loci where despite SNP objects present at the locus, all sites were fixed in the
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focal populations.
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Bugfix: Some haplotypes could pass through the filter, even after particular SNPs were filtered from them.
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Bufgix: Corrected the samples per locus and absent-samples per locus distributions from populations.
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Bugfix: the --write-random-snp flag was causing an infinite loop in populations.
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Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed
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before they are processed.
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Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces
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--min-kmer-freq which is now deprecated
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Bugfix: Fixed a breaking circumstantial segmentation fault in populations
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Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.
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-------------------------------------------------------------------
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Thu Jul 12 10:57:41 UTC 2018 - flyos@mailoo.org
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- Update to 2.1
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- Fixed issue with shebang in perl and python files
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- Cleaned spec file using spec-cleaner
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-------------------------------------------------------------------
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Fri Jan 20 00:17:23 UTC 2017 - flyos@mailoo.org
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- Update to 1.44
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- Enabled SparseHash feature
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- Clean samtools dependency
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-------------------------------------------------------------------
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Sat Apr 30 16:25:54 UTC 2016 - flyos@mailoo.org
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- Cleaner spec file
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-------------------------------------------------------------------
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Thu Apr 21 15:06:46 UTC 2016 - flyos@mailoo.org
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- Changed "./configure" and "make install" for "%configure" and "%make_install"
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-------------------------------------------------------------------
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Wed Apr 20 19:04:22 UTC 2016 - flyos@mailoo.org
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Initial release.-
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