pyrad 3.0.66

@dereneaton dereneaton released this Apr 14, 2016 · 1 commit to master since this release

  • Bug Fix to alleles phased output
  • Loci format changed back to older style with |n| endings, for easier parsing.

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pyrad 3.0.65

@dereneaton dereneaton released this Mar 28, 2016 · 2 commits to master since this release

Major bug fix

  • I had accidentally left a shorter test loop in the step7 code of v.3.0.64, so that only the first 50K loci were written to the phylip & nexus outputs. If you had >50K loci in your assembly then your phylip file was not as large as it should have been. You can re-run step7 in v.3.0.65 to fix this.

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pyrad 3.0.64

@dereneaton dereneaton released this Feb 10, 2016 · 5 commits to master since this release

Bug fixes:

  • Fix to chunk splitter for faster muscle aligning (was sometimes crashing when split wrong)
  • Fix to bi-allelic SNP counter (was not counting correctly, and giving negative numbers sometimes)

Improvements

  • Outputs partition file along with .phy output

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pyrad 3.0.63

@dereneaton dereneaton released this Oct 29, 2015 · 8 commits to master since this release

pyrad 3.0.63 release.

New features

  • loci format contains id numbers of loci before and after filtering for easier matching with consensus reads for various post-assembly analyses.
  • depth data output to files in the clust directory. Useful for plotting.

Bug fixes

  • fix to crash in D-statistics tests
  • fix to loss of loci in alignment on parallel chunk introduced recently during memory consumption fixes.
  • catch error if fail in phynex output builds

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pyrad 3.0.61

@dereneaton dereneaton released this Sep 11, 2015 · 23 commits to master since this release

Updates to pip-install branch with features from deprecated 3.0.5-branch.

New features:

  • Greatly reduced memory load (<1GB) for phy/nex/SNP outputs

Bug fix

  • D-statistic functions work on numbered loci files

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pyrad 3.0.6

@dereneaton dereneaton released this May 27, 2015 · 29 commits to master since this release

New recommended pip install method.

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pyrad 3.0.52

@dereneaton dereneaton released this May 27, 2015 · 29 commits to master since this release

Update to the 3.0.5 branch.

  • Greatly decreased memory load when building nex and phylip files to prevent memory crash on super large data sets.

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pyrad 3.0.51

@dereneaton dereneaton released this May 27, 2015 · 29 commits to master since this release

pyrad 3.0.51

Most development has moved on to 3.1, but until that major release it ready this update to 3.0.5 will be useful to several people with very large data sets. In particular the memory overhead in step 7 has been reduced dramatically and speed improved.

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pyRAD v.3.0.5

@dereneaton dereneaton released this Mar 25, 2015 · 67 commits to master since this release

New features

  • Gphocs output format (f)
  • Better error reporting for misnamed files.
  • Increased max length of sample names from 50 char to 100.
  • vsearch called with subprocess rather than os.system. Better security, and slightly faster.
  • Better re-naming of files that have PEAR naming conventions.

Bug fix

  • Group ids compatible with -s6 and -s7 run together or separately.

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pyRAD v.3.0.4

@dereneaton dereneaton released this Mar 2, 2015 · 79 commits to master since this release

New Features

  • Support for 2B-RAD datatype
  • Numbered loci in .loci output
  • Improved assembly and edge trimming for merged paired reads
  • Updated tutorials for PE-ddRAD and PE-GBS w/ merged reads

Bug Fixes

  • Fix for vsearch crash on seqs shorter than 32bp in step 6

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