Commit upstream/0.15.2+dfsg - aegean

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CHANGELOG.md less more

1	1	All notable changes to this project will be documented in this file.
2	2	This project adheres to [Semantic Versioning](http://semver.org/).
3	3
	4	## [0.15.2] - 2016-03-17
	5
	6	### Fixed
	7	- Minor typo in AgnLocus class.
	8	- Correct reporting of iLocus type.
4	9
5	10	## [0.15.1] - 2016-01-08
6	11

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README.md less more

1	1
2	2	AEGeAn: <b>a</b>nalysis and <b>e</b>valuation of <b>ge</b>nome <b>an</b>notations
3	3
4		Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS.
	4	Copyright (c) 2010-2016, Daniel S. Standage and [CONTRIBUTORS](https://github.com/BrendelGroup/AEGeAn/blob/master/docs/contrib.rst).
5	5	See LICENSE and for details.
6		Project homepage: http://standage.github.io/AEGeAn.
	6	Project homepage: http://brendelgroup.github.io/AEGeAn.
7	7
8		[![AEGeAn build status](https://api.travis-ci.org/standage/AEGeAn.svg?branch=master)](https://travis-ci.org/standage/AEGeAn)
9		[![Coverity Scan build status](https://scan.coverity.com/projects/1021/badge.svg)](https://scan.coverity.com/projects/1021)
	8	[![AEGeAn build status](https://api.travis-ci.org/BrendelGroup/AEGeAn.svg?branch=master)](https://travis-ci.org/BrendelGroup/AEGeAn)
10	9	[![ReadTheDocs build status](https://readthedocs.org/projects/aegean/badge/?version=latest)](https://readthedocs.org/projects/aegean/badge/?version=latest)
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VERSION less more

0		v0.15.1 stable
	0	v0.15.2 stable

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data/gff3/aech-dachsous-out.gff3 less more

5	5	#!genome-build-accession NCBI_Assembly:GCF_000204515.1
6	6	#!annotation-date
7	7	#!annotation-source NCBI Acromyrmex echinatior Annotation Release 100
8		NW_011626563.1 AEGeAn::LocusPocus locus 1190754 1200781 . . . child_gene=1;child_mRNA=2;riil=769;effective_length=10028;iLocus_type=piLocus
	8	NW_011626563.1 AEGeAn::LocusPocus locus 1190754 1200781 . . . child_gene=1;child_mRNA=2;riil=769;effective_length=10028;iLocus_type=siLocus
9	9	NW_011626563.1 AEGeAn::LocusPocus locus 1200782 1201550 . . . fg_orient=FR;effective_length=769;iLocus_type=iiLocus
10		NW_011626563.1 AEGeAn::LocusPocus locus 1201551 1566216 . . . effective_length=364666;iiLocus_exception=complex-overlap-3;liil=769;riil=8884;iLocus_type=piLocus;child_gene=1;child_mRNA=1
11		NW_011626563.1 AEGeAn::LocusPocus locus 1216473 1219475 . . . iiLocus_exception=intron-gene;liil=0;riil=0;iLocus_type=piLocus;child_gene=1;child_mRNA=2
	10	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
	11	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
12	12	NW_011626563.1 AEGeAn::LocusPocus locus 1537022 1540189 . . . liil=0;riil=0;iLocus_type=niLocus;child_gene=1;child_ncRNA=1
13	13	NW_011626563.1 AEGeAn::LocusPocus locus 1566217 1575100 . . . fg_orient=RR;effective_length=8884;iLocus_type=iiLocus
14		NW_011626563.1 AEGeAn::LocusPocus locus 1575101 1579176 . . . liil=8884;child_gene=1;child_mRNA=1;effective_length=4076;iLocus_type=piLocus
	14	NW_011626563.1 AEGeAn::LocusPocus locus 1575101 1579176 . . . liil=8884;child_gene=1;child_mRNA=1;effective_length=4076;iLocus_type=siLocus

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data/gff3/amel-lsm-out-cds.gff3 less more

5	5	#!genome-build-accession NCBI_Assembly:GCF_000002195.4
6	6	#!annotation-date 7 January 2014
7	7	#!annotation-source NCBI Apis mellifera Annotation Release 102
8		NC_007079.3 AEGeAn::LocusPocus locus 8269827 8271756 . . . effective_length=3352;iiLocus_exception=gene-overlap-gene;riil=0;iLocus_type=piLocus;child_gene=1;child_mRNA=1
9		NC_007079.3 AEGeAn::LocusPocus locus 8270498 8273178 . . . liil=0;iLocus_type=piLocus;child_gene=1;child_mRNA=1
	8	NC_007079.3 AEGeAn::LocusPocus locus 8269827 8271756 . . . effective_length=3352;iiLocus_exception=gene-overlap-gene;riil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=1
	9	NC_007079.3 AEGeAn::LocusPocus locus 8270498 8273178 . . . liil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=1

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data/gff3/amel-plap-out-cds.gff3 less more

5	5	#!genome-build-accession NCBI_Assembly:GCF_000002195.4
6	6	#!annotation-date 7 January 2014
7	7	#!annotation-source NCBI Apis mellifera Annotation Release 102
8		NC_007077.3 AEGeAn::LocusPocus locus 8815135 8818920 . . . effective_length=7198;iiLocus_exception=gene-overlap-gene;riil=0;iLocus_type=piLocus;child_gene=1;child_mRNA=1
9		NC_007077.3 AEGeAn::LocusPocus locus 8817660 8822332 . . . liil=0;iLocus_type=piLocus;child_gene=1;child_mRNA=1
	8	NC_007077.3 AEGeAn::LocusPocus locus 8815135 8818920 . . . effective_length=7198;iiLocus_exception=gene-overlap-gene;riil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=1
	9	NC_007077.3 AEGeAn::LocusPocus locus 8817660 8822332 . . . liil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=1

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data/gff3/ilocus.out.noskipends.gff3 less more

24	24	##sequence-region seq24 1 800
25	25	##sequence-region seq25 1 799
26	26	seq01 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1
27		seq02 AEGeAn::LocusPocus locus 1 200 . . . fragment=true
	27	seq02 AEGeAn::LocusPocus locus 1 200 . . . .
28	28	seq02 AEGeAn::LocusPocus locus 201 900 . . . child_gene=1;child_mRNA=1
29		seq03 AEGeAn::LocusPocus locus 1 201 . . . fragment=true
	29	seq03 AEGeAn::LocusPocus locus 1 201 . . . .
30	30	seq03 AEGeAn::LocusPocus locus 202 900 . . . child_gene=1;child_mRNA=1
31	31	seq04 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1
32	32	seq05 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1

34	34	seq07 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;riil=201
35	35	seq07 AEGeAn::LocusPocus locus 801 1001 . . . fg_orient=FF
36	36	seq07 AEGeAn::LocusPocus locus 1002 1600 . . . liil=201;child_gene=1;child_mRNA=1
37		seq07 AEGeAn::LocusPocus locus 1601 2000 . . . fragment=true
	37	seq07 AEGeAn::LocusPocus locus 1601 2000 . . . .
38	38	seq08 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;riil=200
39	39	seq08 AEGeAn::LocusPocus locus 801 1000 . . . fg_orient=FF
40	40	seq08 AEGeAn::LocusPocus locus 1001 1600 . . . liil=200;child_gene=1;child_mRNA=1
41		seq08 AEGeAn::LocusPocus locus 1601 2000 . . . fragment=true
	41	seq08 AEGeAn::LocusPocus locus 1601 2000 . . . .
42	42	seq09 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1;iiLocus_exception=delta-re-extend;riil=0
43	43	seq09 AEGeAn::LocusPocus locus 901 1600 . . . liil=0;child_gene=1;child_mRNA=1
44		seq09 AEGeAn::LocusPocus locus 1601 2000 . . . fragment=true
	44	seq09 AEGeAn::LocusPocus locus 1601 2000 . . . .
45	45	seq10 AEGeAn::LocusPocus locus 1 801 . . . child_gene=1;child_mRNA=1;iiLocus_exception=delta-re-extend;riil=0
46	46	seq10 AEGeAn::LocusPocus locus 802 1500 . . . liil=0;child_gene=1;child_mRNA=1
47		seq10 AEGeAn::LocusPocus locus 1501 2000 . . . fragment=true
	47	seq10 AEGeAn::LocusPocus locus 1501 2000 . . . .
48	48	seq11 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;iiLocus_exception=delta-re-extend;riil=0
49	49	seq11 AEGeAn::LocusPocus locus 801 1500 . . . liil=0;child_gene=1;child_mRNA=1
50		seq11 AEGeAn::LocusPocus locus 1501 2000 . . . fragment=true
	50	seq11 AEGeAn::LocusPocus locus 1501 2000 . . . .
51	51	seq12 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=1;iiLocus_exception=delta-overlap-delta;riil=0
52	52	seq12 AEGeAn::LocusPocus locus 800 1500 . . . left_overlap=1;liil=0;child_gene=1;child_mRNA=1
53		seq12 AEGeAn::LocusPocus locus 1501 2000 . . . fragment=true
	53	seq12 AEGeAn::LocusPocus locus 1501 2000 . . . .
54	54	seq13 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=198;iiLocus_exception=delta-overlap-delta;riil=0
55	55	seq13 AEGeAn::LocusPocus locus 603 1300 . . . left_overlap=198;liil=0;child_gene=1;child_mRNA=1
56		seq13 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
	56	seq13 AEGeAn::LocusPocus locus 1301 1500 . . . .
57	57	seq14 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=199;iiLocus_exception=delta-overlap-delta;riil=0
58	58	seq14 AEGeAn::LocusPocus locus 602 1300 . . . left_overlap=199;liil=0;child_gene=1;child_mRNA=1
59		seq14 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
	59	seq14 AEGeAn::LocusPocus locus 1301 1500 . . . .
60	60	seq15 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=200;iiLocus_exception=delta-overlap-delta;riil=0
61	61	seq15 AEGeAn::LocusPocus locus 601 1300 . . . left_overlap=200;liil=0;child_gene=1;child_mRNA=1
62		seq15 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
	62	seq15 AEGeAn::LocusPocus locus 1301 1500 . . . .
63	63	seq16 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=201;iiLocus_exception=delta-overlap-gene;riil=0
64	64	seq16 AEGeAn::LocusPocus locus 600 1300 . . . left_overlap=201;liil=0;child_gene=1;child_mRNA=1
65		seq16 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
	65	seq16 AEGeAn::LocusPocus locus 1301 1500 . . . .
66	66	seq17 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=395;iiLocus_exception=delta-overlap-gene;riil=0
67	67	seq17 AEGeAn::LocusPocus locus 406 1200 . . . left_overlap=395;liil=0;child_gene=1;child_mRNA=1
68		seq17 AEGeAn::LocusPocus locus 1201 1500 . . . fragment=true
	68	seq17 AEGeAn::LocusPocus locus 1201 1500 . . . .
69	69	seq18 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=399;iiLocus_exception=delta-overlap-gene;riil=0
70	70	seq18 AEGeAn::LocusPocus locus 402 1200 . . . left_overlap=399;liil=0;child_gene=1;child_mRNA=1
71		seq18 AEGeAn::LocusPocus locus 1201 1500 . . . fragment=true
	71	seq18 AEGeAn::LocusPocus locus 1201 1500 . . . .
72	72	seq19 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=400;iiLocus_exception=delta-overlap-gene;riil=0
73	73	seq19 AEGeAn::LocusPocus locus 401 1200 . . . left_overlap=400;liil=0;child_gene=1;child_mRNA=1
74		seq19 AEGeAn::LocusPocus locus 1201 1500 . . . fragment=true
	74	seq19 AEGeAn::LocusPocus locus 1201 1500 . . . .
75	75	seq20 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1
76		seq20 AEGeAn::LocusPocus locus 801 1001 . . . fragment=true
	76	seq20 AEGeAn::LocusPocus locus 801 1001 . . . .
77	77	seq21 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1
78		seq21 AEGeAn::LocusPocus locus 801 1000 . . . fragment=true
	78	seq21 AEGeAn::LocusPocus locus 801 1000 . . . .
79	79	seq22 AEGeAn::LocusPocus locus 1 999 . . . child_gene=1;child_mRNA=1
80	80	seq23 AEGeAn::LocusPocus locus 1 801 . . . child_gene=1;child_mRNA=1
81	81	seq24 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1

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

5	5	#!genome-build-accession NCBI_Assembly:GCF_000220905.1
6	6	#!annotation-date 7 April 2015
7	7	#!annotation-source NCBI Megachile rotundata Annotation Release 101
8		NW_003797177.1 AEGeAn::LocusPocus locus 9652 19311 . . . effective_length=9660;iLocus_type=piLocus;child_gene=1;child_mRNA=1
9		NW_003797177.1 AEGeAn::LocusPocus locus 11405 18146 . . . iiLocus_exception=intron-gene;iLocus_type=piLocus;child_gene=1;child_mRNA=4
	8	NW_003797177.1 AEGeAn::LocusPocus locus 9652 19311 . . . effective_length=9660;iLocus_type=siLocus;child_gene=1;child_mRNA=1
	9	NW_003797177.1 AEGeAn::LocusPocus locus 11405 18146 . . . iiLocus_exception=intron-gene;iLocus_type=siLocus;child_gene=1;child_mRNA=4

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data/gff3/nvit-exospindle-out.gff3 less more

5	5	#!genome-build-accession NCBI_Assembly:GCF_000002325.3
6	6	#!annotation-date 3 June 2014
7	7	#!annotation-source NCBI Nasonia vitripennis Annotation Release 101
8		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=piLocus
9		NC_015867.2 AEGeAn::LocusPocus locus 372891 380536 . . . effective_length=6758;iLocus_type=piLocus;child_gene=1;child_mRNA=1
10		NC_015867.2 AEGeAn::LocusPocus locus 374998 378903 . . . iiLocus_exception=intron-gene;iLocus_type=piLocus;child_gene=1;child_mRNA=1
11		NC_015867.2 AEGeAn::LocusPocus locus 379649 381835 . . . left_overlap=888;liil=0;child_gene=1;child_mRNA=1;effective_length=2187;iLocus_type=piLocus
	8	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
	9	NC_015867.2 AEGeAn::LocusPocus locus 372891 380536 . . . effective_length=6758;iLocus_type=siLocus;child_gene=1;child_mRNA=1
	10	NC_015867.2 AEGeAn::LocusPocus locus 374998 378903 . . . iiLocus_exception=intron-gene;iLocus_type=siLocus;child_gene=1;child_mRNA=1
	11	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

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data/scripts/miloci.py less more

0	0	#!/usr/bin/env python
1	1
2		# Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
	2	# Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
3	3	#
4	4	# The AEGeAn Toolkit is distributed under the ISC License. See
5	5	# the 'LICENSE' file in the AEGeAn source code distribution or

44	44	attrs[key] = 0
45	45	attrs[key] += value
46	46
47		attrstring = 'merged=true;iLocus_type=miLocus'
	47	attrstring = 'iLocus_type=miLocus'
48	48	for key in sorted(attrs):
49	49	attrstring += ';%s=%d' % (key, attrs[key])
50	50	gff3 = [seqid, 'AEGeAn::miloci.py', 'locus', str(start), str(end),

81	81	if len(prev_loci) > 0:
82	82	yield merge_iloci(prev_loci)
83	83	prev_loci = []
84		line = re.sub('ID=[^;\n]+;*', 'geneless=true;', line)
	84	line = re.sub('ID=[^;\n]+;*', '', line)
85	85	line = re.sub('Name=[^;\n]+;*', '', line)
86	86	yield line
87	87	if len(prev_loci) > 0:

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data/scripts/uloci.py less more

0	0	#!/usr/bin/env python
1	1
2		# Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
	2	# Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
3	3	#
4	4	# The AEGeAn Toolkit is distributed under the ISC License. See
5	5	# the 'LICENSE' file in the AEGeAn source code distribution or

110	110	for seqid, seqlen in parse_gff3(args.infile):
111	111	locid = args.idfmt % args.counter
112	112	args.counter += 1
113		attrs = 'ID=%s;Name=%s;fragment=true;unannot=true;' % (locid, locid)
114		attrs += 'iLocus_type=iiLocus;effective_length=%d' % seqlen
	113	attrs = 'ID=%s;Name=%s;unannot=true;' % (locid, locid)
	114	attrs += 'iLocus_type=fiLocus;effective_length=%d' % seqlen
115	115	fields = [seqid, args.src, 'locus', '1', str(seqlen), '.', '.', '.',
116	116	attrs]
117	117	print(*fields, sep='\t')

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docs/contrib.rst less more

3	3	contributed to its code base.
4	4
5	5	* Daniel S. Standage <daniel.standage@gmail.com>, primary developer
6		* Volker Brendel <vbrendel@indiana.edu>, supervision and testing
	6	* Volker Brendel <vbrendel@indiana.edu>, intellectual development, supervision,
	7	and testing
7	8	* Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de> and Gordon Gremme
8	9	<gordon@gremme.org>, integration with GenomeTools, including code examples
9	10	and implementing feature requests

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src/core/AgnLocus.c less more

343	343	break;
344	344	default:
345	345	desc = NULL;
346		fprintf(stderr, "error: unknow comp classification %d\n", c);
	346	fprintf(stderr, "error: unknown comp classification %d\n", c);
347	347	break;
348	348	}
349	349	desc->comparison_count++;

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src/core/AgnLocusRefineStream.c less more

0	0	/**
1	1
2		Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
	2	Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
3	3
4	4	The AEGeAn Toolkit is distributed under the ISC License. See
5	5	the 'LICENSE' file in the AEGeAn source code distribution or

181	181	if(elen)
182	182	test1a = strcmp(elen, "11466") == 0;
183	183	gt_genome_node_delete(locus);
184
	184
185	185	locus = gt_queue_get(queue);
186	186	locusrange = gt_genome_node_get_range(locus);
187	187	test1 = test1 && locusrange.start == 1916352 && locusrange.end == 1927323;
188	188	gt_genome_node_delete(locus);
189
	189
190	190	locus = gt_queue_get(queue);
191	191	locusrange = gt_genome_node_get_range(locus);
192	192	test1 = test1 && locusrange.start == 1918157 && locusrange.end == 1921155;

210	210	if(elen)
211	211	test2a = strcmp(elen, "9660") == 0;
212	212	gt_genome_node_delete(locus);
213
	213
214	214	locus = gt_queue_get(queue);
215	215	locusrange = gt_genome_node_get_range(locus);
216	216	test2 = test2 && locusrange.start == 11405 && locusrange.end == 18146;

292	292	gt_array_delete(exons);
293	293	return false;
294	294	}
295
	295
296	296	GtUword i;
297	297	bool overlap = false;
298	298	for(i = 0; i < gt_array_size(exons); i++)

367	367	gnrange.end = origrange.end;
368	368	else
369	369	gnrange.end += stream->delta;
370
	370
371	371	agn_locus_set_range(*gn, gnrange.start, gnrange.end);
372	372	agn_assert(gt_range_contains(&origrange, &gnrange));
373	373	gt_feature_node_set_source(fn, stream->source);

417	417	break;
418	418	}
419	419	}
420
	420
421	421	// If the iLoci are all coding or all non-coding, just assign their collective
422	422	// length (sans overlap from previous unrefined iLocus) to the first refined
423	423	// iLocus.

448	448	}
449	449	}
450	450	}
451		const char *typestr = "piLocus";
	451	const char *typestr = "siLocus";
452	452	if(coding_status == false)
453	453	typestr = "niLocus";
454	454	else if(agn_locus_num_genes(*gn) > 1)
455	455	{
456		typestr = "complex";
	456	typestr = "ciLocus";
457	457
458	458	char exceptstr[32];
459	459	GtUword genenum = agn_typecheck_count(origfn, agn_typecheck_gene);

491	491	bool cds1 = agn_locus_num_mrnas(*gn1) > 0;
492	492	if(cds1 == true)
493	493	{
494		gt_feature_node_add_attribute(fn1, "iLocus_type", "piLocus");
	494	gt_feature_node_add_attribute(fn1, "iLocus_type", "siLocus");
495	495	gt_feature_node_add_attribute(fn2, "iLocus_type", "niLocus");
496	496	}
497	497	else
498	498	{
499	499	gt_feature_node_add_attribute(fn1, "iLocus_type", "niLocus");
500		gt_feature_node_add_attribute(fn2, "iLocus_type", "piLocus");
	500	gt_feature_node_add_attribute(fn2, "iLocus_type", "siLocus");
501	501	}
502	502
503	503	const char *exc = gt_feature_node_get_attribute(fn2, "iiLocus_exception");

523	523	gt_feature_node_add_attribute(fn1, "riil", orig_riil);
524	524	}
525	525	}
526
	526
527	527	// The genes overlap
528	528	else
529	529	{

610	610	gt_feature_node_add_attribute(fn, "riil", "0");
611	611	}
612	612
613		const char *type = "complex";
614		if(agn_locus_num_genes(*gn) == 1)
615		{
616		if(agn_locus_num_mrnas(*gn) > 0)
617		type = "piLocus";
618		else
619		type = "niLocus";
620
	613	const char *type = "";
	614	if(agn_locus_num_mrnas(*gn) == 0)
	615	{
	616	type = "niLocus";
	617	}
	618	else if(agn_locus_num_genes(*gn) == 1)
	619	{
	620	type = "siLocus";
	621	}
	622	else
	623	{
	624	type = "ciLocus";
621	625	}
622	626	gt_feature_node_add_attribute(fn, "iLocus_type", type);
623	627	}

654	658	sprintf(lenstr, "%lu", gt_range_length(&rng) - ro);
655	659	gt_feature_node_add_attribute(locus, "effective_length", lenstr);
656	660
657		if(gt_feature_node_number_of_children(locus) == 0)
658		gt_feature_node_add_attribute(locus, "iLocus_type", "iiLocus");
659		else if(agn_locus_num_mrnas(gn) > 0)
660		gt_feature_node_add_attribute(locus, "iLocus_type", "piLocus");
	661	const char *loctype = gt_genome_node_get_user_data(gn, "iLocus_type");
	662	if(loctype == NULL)
	663	{
	664	if(gt_feature_node_number_of_children(locus) == 0)
	665	gt_feature_node_add_attribute(locus, "iLocus_type", "iiLocus");
	666	else if(agn_locus_num_mrnas(gn) > 0)
	667	gt_feature_node_add_attribute(locus, "iLocus_type", "siLocus");
	668	else
	669	gt_feature_node_add_attribute(locus, "iLocus_type", "niLocus");
	670	}
661	671	else
662		gt_feature_node_add_attribute(locus, "iLocus_type", "niLocus");
	672	{
	673	gt_feature_node_add_attribute(locus, "iLocus_type", loctype);
	674	}
663	675	gt_queue_add(stream->locusqueue, locus);
664	676	return 0;
665	677	}

+13

-15

src/core/AgnLocusStream.c less more

0	0	/**
1	1
2		Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
	2	Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
3	3
4	4	The AEGeAn Toolkit is distributed under the ISC License. See
5	5	the 'LICENSE' file in the AEGeAn source code distribution or

261	261	locusrange.end);
262	262	if(stream->endmode >= 0 && !stream->skip_iiLoci)
263	263	{
264		AgnLocus *iilocus = agn_locus_new(seqid);
265		GtRange irange = { seqrange.start,
266		locusrange.start - stream->delta - 1 };
267		agn_locus_set_range(iilocus, irange.start, irange.end);
268		GtFeatureNode *iilocfn = gt_feature_node_cast(iilocus);
269		gt_feature_node_add_attribute(iilocfn, "fragment", "true");
270		gt_queue_add(stream->locusqueue, iilocus);
	264	AgnLocus *filocus = agn_locus_new(seqid);
	265	GtRange irange = {seqrange.start, locusrange.start - stream->delta - 1};
	266	agn_locus_set_range(filocus, irange.start, irange.end);
	267	gt_genome_node_add_user_data(filocus, "iLocus_type",
	268	gt_cstr_dup("fiLocus"), gt_free_func);
	269	gt_queue_add(stream->locusqueue, filocus);
271	270	}
272	271	}
273	272	else

396	395	locusrange.end + stream->delta);
397	396	if(stream->endmode >= 0 && !stream->skip_iiLoci)
398	397	{
399		AgnLocus *term_locus = agn_locus_new(seqid);
400		agn_locus_set_range(term_locus,
401		locusrange.end + stream->delta + 1, seqrange.end);
402		GtFeatureNode tlfn = (GtFeatureNode )term_locus;
403		gt_feature_node_add_attribute(tlfn, "fragment", "true");
404		gt_queue_add(stream->locusqueue, term_locus);
	398	AgnLocus *filocus = agn_locus_new(seqid);
	399	GtRange irange = {locusrange.end + stream->delta + 1, seqrange.end};
	400	agn_locus_set_range(filocus, irange.start, irange.end);
	401	gt_genome_node_add_user_data(filocus, "iLocus_type",
	402	gt_cstr_dup("fiLocus"), gt_free_func);
	403	gt_queue_add(stream->locusqueue, filocus);
405	404	}
406	405	}
407	406	else

862	861
863	862	gt_queue_delete(queue);
864	863	}
865