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Commits on Apr 19, 2024

• match source and type with regex and set defaults

  thackl

  committed
  82aed01

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• masked ";" in note when converting to gff

  thackl

  committed
  64c9c35

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• handle windows line ends

  thackl

  committed
  c4425dd

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• compute complement index on the fly

  thackl

  committed
  c61e2b1

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• better dir handling

  thackl

  committed
  faffd55

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• added seq-circ-restart for reorienting/restarting circular chromosomes at marker gene

  thackl

  committed
  77a7be9

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Commits on May 16, 2023

• doc options for seq-polish

  thackl

  committed
  6c635fc

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Commits on May 20, 2022

• added flye-post for postprocessing flye assemblies

  thackl

  committed
  77351e3

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Commits on Oct 15, 2021

• fix regex

  thackl

  committed
  adc79a1

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• send final fasta through seqkit to get multiline fasta

  thackl

  committed
  25fa38a

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• codontable in gff2cds

  thackl

  committed
  a7bfc3b

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• dont remove trailing nums from contigs - this breaks metagenomes

  thackl

  committed
  51381c5

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Commits on Oct 14, 2021

• thread medaka at subscript level; filter min length; use run()

  thackl

  committed
  4910f5a

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Commits on Oct 13, 2021

• fixed thread option

  thackl

  committed
  54f50ac

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• added seq-polish to run iterations of racon and medaka

  thackl

  committed
  2038b1a

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Commits on Jul 27, 2021

• add column for query length

  thackl

  committed
  5ca4688

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Commits on Jul 14, 2021

• create dirs for output paths

  thackl

  committed
  93afe93

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• small fix

  thackl

  committed
  8d8c4a9

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• more options for seq-split - min-group-size, variable group fields

  thackl

  committed
  6f5d5ac

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Commits on Jun 25, 2021

• add file name to seq-ids output

  thackl

  committed
  82de1c5

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Commits on Feb 14, 2021

• use hidden temp files to avoid collision with output file names

  thackl

  committed
  0585b2e

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Commits on Feb 12, 2021

• seq-chop is much faster than seq-frag for just creating equal-sized chops

  thackl

  committed
  6ff990e

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Commits on Feb 2, 2021

• seq-len now also works on fastq

  thackl

  committed
  d0935a9

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• add error message

  thackl

  committed
  e3826c8

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Commits on Jan 29, 2021

• gbk support for seq-len

  thackl

  committed
  a8b25dc

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• add --fasta option for seqs from ORIGIN only

  thackl

  committed
  f401310

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• seq-len parser for fasta/gff and gbk via gb2gff conversion

  thackl

  committed
  53779c8

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Commits on Jan 21, 2021

• gb2gff parser with Parent inference

  thackl

  committed
  d66ea09

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Commits on Jan 8, 2021

• standalone, comprehensive reimplementation of gb2gff

  thackl

  committed
  1aa7919

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Commits on Nov 3, 2020

• get strand right in --query mode

  thackl

  committed
  a6a472c

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Commits on Jan 22, 2020

• read from multiple files at once

  thackl

  committed
  0c9039e

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Commits on Oct 23, 2019

• fix prodigal issues and give more control on feature numbering

  thackl

  committed
  cfa4562

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• really fix regex for non-existing Name tag

  thackl

  committed
  b9f902b

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• fix regex for non-existing Name tag

  thackl

  committed
  654cccd

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• reset counter on each new contig

  thackl

  committed
  3a14080

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