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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 12:56:18 -0500
parents 99d0b19ef534
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99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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1 Stacks 2.2 - Aug 22, 2018
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2 --------------------------
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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3 Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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4 before they are processed.
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5 Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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6 --min-kmer-freq which is now deprecated
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7 Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.
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8
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9 Stacks 2.1 - June 25, 2018
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10 --------------------------
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11 Bugfix: Fixed a performance regression in sstacks. Recent changes in sstacks made it more likely to
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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12 invoke the gapped algorithm to match to the catalog. In some cases, matches to the catalog
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13 would be marked as ambiguous alignments and dropped from the next stages of analysis due to
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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14 differences in CIGAR strings from the gapped alignment.
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15 Feature: ustacks Changed --high_cov_thres default value from 2.0 to 3.0.
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16 Feature: gstacks: Changed --min-kmer-freq default value from 0.05 to 0.01.
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17 Feature: Added further checks on zlib calls.
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18
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19 Stacks 2.0 - Apr 23, 2018
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20 -------------------------
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21 Feature: modified cstacks and ustacks gapped alignment algorithms to always align the two stacks/alleles
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22 with the most k-mers in common, removed the previous minimum k-mer limit.
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23 Feature: modified cstacks so that when a sample locus matches two or more catalog loci, those catalog
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24 loci are combined, or rolled-up, reducing undermerged loci that generate excess homozygote calls.
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25 Feature: modified tsv2bam so that when two loci from the same sample match the same catalog locus, those
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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26 loci are combined.
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27 Bugfix: corrected BbvCI restriction enzyme to add the missing negative strand sequence.
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28 Bugfix: corrected the catalog writing routines for unzipped output files to include missing column.
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29 Bugfix: populations: Fixed the filtering of monomorphic loci.
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30 Bugfix: populations: Now preserving sample ordering in all outputs.
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31 Bugfix: Fixed ICPC compilation.
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32
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33 2.0b - May 1, 2018
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34 Feature: gstacks: Removed the assertion that the first basepair of each locus should
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35 be part of a cutsite (now a warning).
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36 Feature: gstacks: The reported effective coverage is now a more realistic weighted mean.
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37 Bugfix: populations: Fixed STRUCTURE output being corrupted for some unordereds population maps.
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38
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39 Stacks 2.0 Beta 10 - Apr 10, 2018
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40 ---------------------------------
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41 Feature: Improved gapped alignment for secondary reads in ustacks.
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42 Feature: Improved populations performance.
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43 Feature: Added enzymes Cac8I, MslI.
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44 Feature: Made population maps more tolerant to spurious extra spaces and lines.
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45 Feature: populations: VCF output: changed the format of the catalog locus field and made the column 1-based.
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46 Feature: gstacks: increased haplotyping rates by adding a filtering of spurious SNPs step.
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47 Bugfix: Fixed populations dramatric slow-down on datasets with more than several hundred samples.
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48 Bugfix: Restored the NS/locus distribution in populations's distributions log.
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49 Bugfix: Fixed the populations --radpainter export.
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50 Bugfix: stacks-dist-extract: Fixed OSX compatibility.
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51 Bugfix: Fixed breaking bug in populations --in-vcf mode filtering statistics.
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52
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53 Stacks 2.0 Beta 9 - Mar 12, 2018
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54 --------------------------------
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55 Feature: Cleaned up tags/snps/alleles/matches files. We removed the batch ID from ustacks and cstacks
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56 output, and the deprecated log likelihood fields from ustacks and cstacks. We also removed
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57 the chromosome/bp/strand fields as they are no longer used in these files.
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58 Feature: Renamed gstacks output files that represent the new components of the catalog:
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59 gstacks.fa.gz => catalog.fa.gz; gstacks.vcf.gz => catalog.calls
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60 Feature: Removed read length restrictions from ustacks/cstacks/sstacks core, reads/loci can vary in
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61 length throughout the pipeline.
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62 Feature: Reimplemented PLINK export format for the populations program.
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63 Bugfix: Updated to HTSLib 1.7; changed to a custom build system that will work with the Stacks build
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64 system.
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65 Bugfix: Made gapped alignments mandatory in ustacks, cstacks, and sstacks. Added check for frameshift
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66 at 3' end of the read -- if found, a match is deferred to the gapped aligner.
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67
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68 Stacks 2.0 Beta 8 - Feb 03, 2018
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69 --------------------------------
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70 Feature: populations: Now calculated deviation from Hardy-Weinberg equilibrium at the SNP level
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71 (using an exact test), and at the haplotype level (using Guo+Thompson's MCMC algorithm).
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72 Feature: populations: Added an export type for FineRADStructure.
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73 Feature: populations: Added the GQ/GL fields in the VCF SNPs output.
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74 Feature: gstacks: Made the default behavior regarding paired-end reads more logical (in
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75 reference-based mode --paired has been replaced with --unpaired).
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76 Feature: gstacks: Added details about samples and coverages to the log outputs.
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77 Feautre: Added enzymes NspI, BbvCI, fixed BfuCI.
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78 Bugfix: corrected a major performance bottleneck in populations when smoothing population statistics
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79 across the genome.
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80 Bugfix: populations: The VCF output now preserves the input sample order.
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81 Bugfix: gstacks: Fixed the handling of a rare special case in the PCR duplicates code.
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82 Bugfix: gstacks: Fixed 100% being added to all per-thread timings.
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83
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84 Stacks 2.0 Beta 7 - Dec 29, 2017
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85 --------------------------------
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86 Feature: gstacks: Added an option to remove PCR duplicates based on insert
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87 size (--rm-pcr-duplicates, plus the related --rm-unpaired-reads).
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88 Feature: populations: Added a haplotype Genepop export.
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89 Feature: populations: improved the help; changed the output names for SNP
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90 files to 'populations.snps.EXT'; added option --no_hap_exports.
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91 Feature: gstacks and populations: Clarified the logs; moved distributions
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92 to a separate '.xlog' file and added script stacks-xlog-extract.
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93 Feature: gstacks: Tweaked the help/interface; especially, replaced --spacer
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94 with --suffix (for BAM directory input).
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95 Feature: Added enzymes BfuI and HinP1.
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96 Feature: Added option --inline_null to clone_filter.
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97 Bugfix: gstacks: Fixed a typo preventing the paired reads from being merged.
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98 Bugfix: populations: Fixed a segfault that occurred with some large datasets.
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99 Bugfix: Made VCF outputs more standard compliant.
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100 Bugfix: populations: Repaired --fasta_samples and --fasta_samples_raw.
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101 Bugfix: populations: Fixed population aborting at the end of the run
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102 when an export option was specified multiple times.
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103 Bugfix: gstacks: Adjusted progression report for catalog asymmetry.
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104 Bugfix: Fixed installation of stacks-integrate-alignments on MacOS.
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105
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106 Stacks 2.0 Beta 6 - Dec 02, 2017
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107 --------------------------------
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108 Feature: Implmented the VCF haplotypes output.
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109 Bugfix: Corrected asset failure in populations when exporting data for genepop or structure output.
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110
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111 Stacks 2.0 Beta 5 - Nov 27, 2017
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112 --------------------------------
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113 Feature: Reimplemented structure, phylip, and phylip_var exports.
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114 Bugfix: Tightened up the overlap algorithm to require 80% of overlapping sequence to be
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115 aligned and of the aligned sequence, 80% must be identities.
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116 Bugfix: Fixed segfault in gstacks when compiled with CLANG on OS X.
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117 Bugfix: gstacks: Fixed how misphasings are reported.
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118
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119 Stacks 2.0 Beta 4 - Nov 07, 2017
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120 --------------------------------
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121 Bugfix: Continued improving overlap algorithm to join SE and PE contigs.
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122 Bugfix: Improved build system to handle new timing functions in gstacks.
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123
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124 Stacks 2.0 Beta 3 - Nov 01, 2017
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125 --------------------------------
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126 Feature: Added output to populations describing mean PE contig size and mean number of
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127 genotyped sites per locus, which reflects the current filtering paramters.
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128 Feature: Improved the output of gstacks and populations.
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129 Feature: Added script `stacks-integrate-alignments`.
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130 Bugfix: made further improvements to the single-end/paired-end locus overlapping algorithm.
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131 Bugfix: fixed all depths being null in populations' VCF output.
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132 Bugfix: Numerically tweaked the marukilow model to remove a limit case.
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133
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134 Stacks 2.0 Beta 2 - Oct 19, 2017
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135 --------------------------------
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136 Feature: gstacks: Made it possible to read from multiple BAM files at the same time; modified the
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137 interface accordingly.
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138 Feature: gstacks: Parallelized the reference-based mode.
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139 Feature: gstacks: Added various statistics & improvements to the log output.
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140 Feature: gstacks: Improved how the forward & paired-end reads are merged (in denovo mode; no more trimming).
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141 Feature: populations: Added code to calculate the overlap between RAD loci when a reference is available.
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142 Feature: populations: Added VCF ouput (--vcf).
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143 Feature: Updated the denovo_map.pl and ref_map.pl wrappers, samples must now be specified using --samples and --popmap.
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144 Bugfix: Fixed three memory leaks in populations; improved reference-aligned batch logic.
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145 Bugfix: Improved overlapping code in gstacks to merge more single and paired-end contigs together.
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146 Bugfix: Now compiles on Apple OS X.
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147 Bugfix: Fixed a bug that skewed the fixed-site (no-SNP) likelihood in the marukilow model.
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148
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149 Stacks 2.0 Beta 1 - Oct 09, 2017
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150 --------------------------------
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151 Feature: Paired-end sequencing data can be utilized fully. In particular, when the shearing-based
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152 protocol is used, the software will assemble a local contig from the paired reads across
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153 the population, possibly overlap it with the forward-reads region, then align all reads to the
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154 assembled contig. This new approach also fully supports double-digest protocols.
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155 Feature: Haplotype calling and diploidy-violation dectection now rely on a novel, more powerful algorithm.
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156 Feature: SNP and genotype-calling now uses the diploid models of Maruki and Lynch (2017).
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157 Feature: The rxstacks program has been replaced with the gstacks program, and there is no need to re-run
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158 some of the earlier steps of the pipeline anymore.
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159 Feature: The memory footprint of the populations program has been considerably reduced and can be scaled
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160 for any size data set.
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161 Feature: The reference-based pipeline has been simplified, and now only comprises two steps: gstacks and populations.
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162 Feature: Added --null_inline mode to clone_filter (and process_radtags) for previously unseen type
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163 of oligo combination.
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164
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165 Stacks 1.48 - Nov 20, 2017
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166 ---------------------------
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167 Feature: Added HinP1I restriction enzyme.
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168 Feature: Added --null_inline mode to clone_filter (and process_radtags) for previously unseen type
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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169 of oligo combination.
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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170
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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171 Stacks 1.47 - Sept 06, 2017
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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172 ---------------------------
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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173 Feature: Improved populations's fasta output options (especially,
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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174 added a option to export locus consensus sequences).
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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175 Feature: denovo_map.pl and red_map.pl now stop if a component
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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176 of the pipeline fails.
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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177 Feature: Improved the output of denovo_map.pl and ref_map.pl.
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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178 Bugfix: Added a format check in Fasta/GzFasta to avoid a potential
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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179 segfault when working on FastQ files.
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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180 Bugfix: Fixed a bug in count_fixed_catalog_snps.py that could cause
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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181 overwrites when working with uncompressed files.