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CHANGELOG.md

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Change Log

Unreleased - ReleaseDate

0.7.7 - 2024-07-19

  • Move ovlpr to anchr
  • Add rgr pl-2rmp
  • Add --group to rgr sort
  • Use MultiGzDecoder in intspan::reader()

0.7.5 - 2023-07-28

  • Add fasr replace

  • Add fasr pl-p2m

  • Add fasr xlsx

  • Add --outgroup to fasr consensus and fasr variation

  • Add --required to fasr subset

  • Add --outgroup, --chop, and --quick to fasr refine

  • Implementing --parallel with crossbeam

    • for fasr consensus
    • for fasr refine

0.7.4 - 2023-07-20

  • Add fasr filter

  • Add fasr refine

  • Add fasr variation

  • Add --multi to fasr create

0.7.3 - 2023-07-18

  • New binary fasr, ported from App::Fasops

    • fasr axt2fas
    • fasr check
    • fasr concat
    • fasr consensus
    • fasr cover
    • fasr create
    • fasr join
    • fasr link
    • fasr maf2fas
    • fasr name
    • fasr separate
    • fasr slice
    • fasr split
    • fasr stat
    • fasr subset

  • Add libs/alignment

  • Add utils::get_seq_faidx()

  • Add IntSpan.find_islands_n() and IntSpan.find_islands_ints()

  • Use json to replace yaml in spanr

  • Bump versions of deps

    • clap v4
    • Use anyhow

0.7.1 - 2022-06-14

  • Store IntSpan.edges in VecDeque
  • Switch to clap v3.2

0.7.0 - 2022-05-23

  • Add rgr sort

  • Add rgr prop

  • Add --fields to rgr field

  • Add --header, --sharp, --field to rgr count and rgr runlist

0.6.9 - 2022-05-15

  • Add rgr field

  • Move spanr range to rgr runlist

  • Move spanr count to rgr count

  • Rename .ranges to .rg

0.6.8 - 2022-05-14

  • New binary rgr

  • Move ovlpr replace to rgr replace

  • Move linkr merge to rgr merge

0.6.7 - 2022-04-24

  • Add spanr count
  • Add --detailed to spanr coverage
  • Use Box<dyn std::error::Error>

0.6.5 - 2022-04-22

  • Use rust_lapper as an intermediate layer instead of intspan::Coverage
    • Greatly improves the speed of spanr coverage

0.6.4 - 2022-04-21

  • Move far out
  • spanr stat use i64 in the all lines
  • Update Github actions
    • Use a container with GLIBC 2.17 to build linux-gnu binary
    • Codecov with cargo-tarpaulin

0.6.0 - 2022-02-22

  • Move nwr out

0.4.17 - 2022-02-21

  • Add nwr download
  • Add nwr txdb
  • Add nwr info
  • Add nwr lineage
  • Add nwr restrict
  • Add nwr member
  • Add nwr append

0.4.16 - 2022-02-12

  • Switch to clap v3
  • New binary nwr

0.4.15 - 2021-08-19

  • Add far some
  • Add slice() to IntSpan
  • ovlpr replace now processes any .tsv files

0.4.14 - 2020-05-15

0.4.13 - 2020-05-15

  • New binary far

0.4.12 - 2020-03-05

  • Split spanr cover into cover and coverage

0.4.11 - 2020-02-15

  • Add --all to spanr merge

0.4.10 - 2020-02-15

  • Add --op to spanr combine

0.4.9 - 2019-12-09

  • Add ovlpr replace

  • Add ovlpr restrict

  • Github Actions publish.yml

0.4.1 - 2019-09-10

  • Add benchmarks.md

  • Add ovlpr paf2ovlp

  • Binary releases by Github Actions

0.4.0 - 2019-09-07

  • New binary ovlpr

  • Struct Overlap

  • Move libraries to libs/

  • Passing &str when calling methods

  • Add new_len() and uniq_tiers() to Coverage

  • Add from_pair() to IntSpan

  • Wrap IO functions in utils.rs with Result

  • Satisfy clippy

0.3.3 - 2019-09-04

  • spanr merge: take the first part of filename
  • spanr compare: compare more than two infiles

0.3.2 - 2019-09-03

  • Add --suffix to spanr split

0.3.1 - 2019-09-03

  • Detailed benchmarks on linkr

  • Make POS_INF, NEG_INF and EMPTY_STRING as lazy_static

  • About 10-20% faster

0.3.0 - 2019-09-03

  • New binary linkr for commands ported from App::Rangeops and jrange

  • Illustrations for some concepts

    • IntSpans
    • Ranges

  • Rename binary intspan to spanr

0.2.0 - 2019-08-24

  • Ported all commands from App::RL and jrunlist
  • Struct Range
  • Struct Coverage
  • Adopt cargo release

0.1.0 - 2019-08-13

  • Struct IntSpan
  • Examples