Commit 96c39eb4 authored Oct 05, 2018 by Sascha Steinbiss

New upstream version 0.16.0+dfsg

parent 6261fb6c

CHANGELOG.md

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		All notable changes to this project will be documented in this file.
		This project adheres to [Semantic Versioning](http://semver.org/).

		## [0.16.0] - 2016-05-09

		### Fixed
		- Outer gene in intron gene cases now designated as a ciLocus.
		- ciLoci are now exempt from merging into miLoci.
		- Fixes to how polycistrons and other edge cases are handled.

		## [0.15.2] - 2016-03-17

		### Fixed

VERSION

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		v0.15.2 stable
		v0.16.0 stable

data/gff3/aech-dachsous-out.gff3

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		#!annotation-source NCBI Acromyrmex echinatior Annotation Release 100
		NW_011626563.1 AEGeAn::LocusPocus locus 1190754 1200781 . . . child_gene=1;child_mRNA=2;riil=769;effective_length=10028;iLocus_type=siLocus
		NW_011626563.1 AEGeAn::LocusPocus locus 1200782 1201550 . . . fg_orient=FR;effective_length=769;iLocus_type=iiLocus
		NW_011626563.1 AEGeAn::LocusPocus locus 1201551 1566216 . . . effective_length=364666;iiLocus_exception=complex-overlap-3;liil=769;riil=8884;iLocus_type=siLocus;child_gene=1;child_mRNA=1
		NW_011626563.1 AEGeAn::LocusPocus locus 1201551 1566216 . . . iLocus_type=ciLocus;effective_length=364666;iiLocus_exception=complex-overlap-3;liil=769;riil=8884;child_gene=1;child_mRNA=1
		NW_011626563.1 AEGeAn::LocusPocus locus 1216473 1219475 . . . iiLocus_exception=intron-gene;liil=0;riil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=2
		NW_011626563.1 AEGeAn::LocusPocus locus 1537022 1540189 . . . liil=0;riil=0;iLocus_type=niLocus;child_gene=1;child_ncRNA=1
		NW_011626563.1 AEGeAn::LocusPocus locus 1566217 1575100 . . . fg_orient=RR;effective_length=8884;iLocus_type=iiLocus

data/gff3/mrot-cst-out-cds.gff3

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		#!genome-build-accession NCBI_Assembly:GCF_000220905.1
		#!annotation-date 7 April 2015
		#!annotation-source NCBI Megachile rotundata Annotation Release 101
		NW_003797177.1 AEGeAn::LocusPocus locus 9652 19311 . . . effective_length=9660;iLocus_type=siLocus;child_gene=1;child_mRNA=1
		NW_003797177.1 AEGeAn::LocusPocus locus 9652 19311 . . . iLocus_type=ciLocus;effective_length=9660;child_gene=1;child_mRNA=1
		NW_003797177.1 AEGeAn::LocusPocus locus 11405 18146 . . . iiLocus_exception=intron-gene;iLocus_type=siLocus;child_gene=1;child_mRNA=4

data/gff3/nvit-exospindle-out.gff3

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		#!annotation-date 3 June 2014
		#!annotation-source NCBI Nasonia vitripennis Annotation Release 101
		NC_015867.2 AEGeAn::LocusPocus locus 370926 373152 . . . child_gene=1;child_mRNA=1;right_overlap=262;iiLocus_exception=delta-overlap-delta;riil=0;effective_length=1965;iLocus_type=siLocus
		NC_015867.2 AEGeAn::LocusPocus locus 372891 380536 . . . effective_length=6758;iLocus_type=siLocus;child_gene=1;child_mRNA=1
		NC_015867.2 AEGeAn::LocusPocus locus 372891 380536 . . . iLocus_type=ciLocus;effective_length=6758;child_gene=1;child_mRNA=1
		NC_015867.2 AEGeAn::LocusPocus locus 374998 378903 . . . iiLocus_exception=intron-gene;iLocus_type=siLocus;child_gene=1;child_mRNA=1
		NC_015867.2 AEGeAn::LocusPocus locus 379649 381835 . . . left_overlap=888;liil=0;child_gene=1;child_mRNA=1;effective_length=2187;iLocus_type=siLocus