@brentp brentp released this Aug 30, 2018 · 1 commit to master since this release

Assets 4

v0.3.0

  • support for NON_REF to match any ALT allele (#92)
  • more work on multiple alts (#87)

there should be ~3-5% speed improvement thanks to improvements in the go compiler.

@brentp brentp released this Mar 26, 2018 · 7 commits to master since this release

Assets 4

this release adds support for CSI. this can greatly speed up dense files like CADD and even gnomAD or ExAC.

to use, simply index your file with tabix as, e.g.:

tabix -m 12 --csi $file

and vcfanno will prefer the .csi index over the .tbi.

refer to the performance page for how to optimize.
in brief, setting

export IRELATE_MAX_GAP=1000

seems to give good results. Please experiment and let me know what works for you. I can get ~60% speed improvement using csi'd ExAC to annotate clinvar with the above changes.

@brentp brentp released this Jul 10, 2017 · 8 commits to master since this release

Assets 4

v0.2.8

  • fix fo #71 for out of bounds warning followed by panic.

@brentp brentp released this Jun 20, 2017 · 12 commits to master since this release

Assets 4

v0.2.7

  • restore multiple threads per annotation file after fix in biogo/hts (#64)
  • new op setid builtin to set the ID field and remove need for lua and fix some bugs.
  • fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
  • fix for #68, #69 -- with Number=A, op="self", the output will always have a number of elements
    equal to the number of alternates. If there are > 1 annos for a given site, later values will
    overwrite previous.
  • new op by_alt that will have Number=A and will append multiple annotations for the same alternate
    (from the same file) and output them as pipe-delimited. e.g with 2 alts, it might look like: 0.111,0.222|0.333
    when the 1st alternate has a single value and the 2nd alternate has 2 values.

@brentp brentp released this Jun 19, 2017 · 15 commits to master since this release

Assets 4

v0.2.7 (dev)

  • restore multiple threads per annotation file after fix in biogo/hts (#64)
  • new op setid builtin to set the ID field and remove need for lua and fix some bugs.
  • fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
  • fix for #68, #69 -- with Number=A, op="self", the output will always have a number of elements
    equal to the number of alternates. If there are > 1 annos for a given site, later values will
    overwrite previous.
  • new op by_alt that will have Number=A and will append multiple annotations for the same alternate
    (from the same file) and output them as pipe-delimited. e.g with 2 alts, it might look like: 0.111,0.222|0.333
    when the 1st alternate has a single value and the 2nd alternate has 2 values.

@brentp brentp released this Jun 15, 2017 · 16 commits to master since this release

Assets 4

v0.2.7 (dev)

  • restore multiple threads per annotation file after fix in biogo/hts (#64)
  • add setid builtin to set the ID field and remove need for lua and fix some bugs.
  • fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
  • fix for #68, #69 -- with Number=A, op="self", the output will always have a number of elements
    equal to the number of alternates. If there are > 1 annos for a given site, later values will
    overwrite previous.

@brentp brentp released this Jun 14, 2017 · 18 commits to master since this release

Assets 4
  • restore multiple threads per annotation file after fix in biogo/hts (#64)
  • add setid builtin to set the ID field and remove need for lua and fix some bugs.
  • fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
  • fix for #68, #69

@brentp brentp released this May 5, 2017 · 23 commits to master since this release

Assets 4

v0.2.6

  • fix race condition from 0.2.4 by reverting some speed improvements from that release.
May 5, 2017
bump version

@brentp brentp released this Mar 27, 2017 · 31 commits to master since this release

Assets 4

v0.2.4

  • 30-40% speed improvement when annotating with few, large files by parallelizing decompression.
  • handle multiple values to div2 (mostly for multi-allelics)
  • if _af or af_ is in the name then make Number=A for a postannotation.