[med-svn] [aegean] 02/09: Imported Upstream version 0.15.2+dfsg
Sascha Steinbiss
sascha at steinbiss.name
Sun Mar 20 11:46:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository aegean.
commit 6261fb6c79c19a9789abb91f072b2f2cf4f0a437
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sun Mar 20 11:30:58 2016 +0000
Imported Upstream version 0.15.2+dfsg
---
CHANGELOG.md | 5 +++
README.md | 8 ++---
VERSION | 2 +-
data/gff3/aech-dachsous-out.gff3 | 8 ++---
data/gff3/amel-lsm-out-cds.gff3 | 4 +--
data/gff3/amel-plap-out-cds.gff3 | 4 +--
data/gff3/ilocus.out.noskipends.gff3 | 34 ++++++++++----------
data/gff3/mrot-cst-out-cds.gff3 | 4 +--
data/gff3/nvit-exospindle-out.gff3 | 8 ++---
data/scripts/miloci.py | 6 ++--
data/scripts/uloci.py | 6 ++--
docs/contrib.rst | 3 +-
src/core/AgnLocus.c | 2 +-
src/core/AgnLocusRefineStream.c | 60 +++++++++++++++++++++---------------
src/core/AgnLocusStream.c | 28 ++++++++---------
15 files changed, 98 insertions(+), 84 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8f0348e..c4fb607 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,11 @@
All notable changes to this project will be documented in this file.
This project adheres to [Semantic Versioning](http://semver.org/).
+## [0.15.2] - 2016-03-17
+
+### Fixed
+- Minor typo in AgnLocus class.
+- Correct reporting of iLocus type.
## [0.15.1] - 2016-01-08
diff --git a/README.md b/README.md
index 9101107..845fd57 100644
--- a/README.md
+++ b/README.md
@@ -2,11 +2,9 @@
AEGeAn: <b>a</b>nalysis and <b>e</b>valuation of <b>ge</b>nome <b>an</b>notations
-Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS.
+Copyright (c) 2010-2016, Daniel S. Standage and [CONTRIBUTORS](https://github.com/BrendelGroup/AEGeAn/blob/master/docs/contrib.rst).
See LICENSE and for details.
-Project homepage: http://standage.github.io/AEGeAn.
+Project homepage: http://brendelgroup.github.io/AEGeAn.
-[](https://travis-ci.org/standage/AEGeAn)
-[](https://scan.coverity.com/projects/1021)
+[](https://travis-ci.org/BrendelGroup/AEGeAn)
[](https://readthedocs.org/projects/aegean/badge/?version=latest)
-
diff --git a/VERSION b/VERSION
index 9dc514f..69ca83a 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v0.15.1 stable
+v0.15.2 stable
diff --git a/data/gff3/aech-dachsous-out.gff3 b/data/gff3/aech-dachsous-out.gff3
index c4bd6b8..f53b144 100644
--- a/data/gff3/aech-dachsous-out.gff3
+++ b/data/gff3/aech-dachsous-out.gff3
@@ -6,10 +6,10 @@
#!genome-build-accession NCBI_Assembly:GCF_000204515.1
#!annotation-date
#!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=piLocus
+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=piLocus;child_gene=1;child_mRNA=1
-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
+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 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
-NW_011626563.1 AEGeAn::LocusPocus locus 1575101 1579176 . . . liil=8884;child_gene=1;child_mRNA=1;effective_length=4076;iLocus_type=piLocus
+NW_011626563.1 AEGeAn::LocusPocus locus 1575101 1579176 . . . liil=8884;child_gene=1;child_mRNA=1;effective_length=4076;iLocus_type=siLocus
diff --git a/data/gff3/amel-lsm-out-cds.gff3 b/data/gff3/amel-lsm-out-cds.gff3
index 3f0b1ba..5b3531d 100644
--- a/data/gff3/amel-lsm-out-cds.gff3
+++ b/data/gff3/amel-lsm-out-cds.gff3
@@ -6,5 +6,5 @@
#!genome-build-accession NCBI_Assembly:GCF_000002195.4
#!annotation-date 7 January 2014
#!annotation-source NCBI Apis mellifera Annotation Release 102
-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
-NC_007079.3 AEGeAn::LocusPocus locus 8270498 8273178 . . . liil=0;iLocus_type=piLocus;child_gene=1;child_mRNA=1
+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
+NC_007079.3 AEGeAn::LocusPocus locus 8270498 8273178 . . . liil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=1
diff --git a/data/gff3/amel-plap-out-cds.gff3 b/data/gff3/amel-plap-out-cds.gff3
index d3fff6f..4627572 100644
--- a/data/gff3/amel-plap-out-cds.gff3
+++ b/data/gff3/amel-plap-out-cds.gff3
@@ -6,5 +6,5 @@
#!genome-build-accession NCBI_Assembly:GCF_000002195.4
#!annotation-date 7 January 2014
#!annotation-source NCBI Apis mellifera Annotation Release 102
-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
-NC_007077.3 AEGeAn::LocusPocus locus 8817660 8822332 . . . liil=0;iLocus_type=piLocus;child_gene=1;child_mRNA=1
+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
+NC_007077.3 AEGeAn::LocusPocus locus 8817660 8822332 . . . liil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=1
diff --git a/data/gff3/ilocus.out.noskipends.gff3 b/data/gff3/ilocus.out.noskipends.gff3
index e869dce..4974f38 100644
--- a/data/gff3/ilocus.out.noskipends.gff3
+++ b/data/gff3/ilocus.out.noskipends.gff3
@@ -25,9 +25,9 @@
##sequence-region seq24 1 800
##sequence-region seq25 1 799
seq01 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1
-seq02 AEGeAn::LocusPocus locus 1 200 . . . fragment=true
+seq02 AEGeAn::LocusPocus locus 1 200 . . . .
seq02 AEGeAn::LocusPocus locus 201 900 . . . child_gene=1;child_mRNA=1
-seq03 AEGeAn::LocusPocus locus 1 201 . . . fragment=true
+seq03 AEGeAn::LocusPocus locus 1 201 . . . .
seq03 AEGeAn::LocusPocus locus 202 900 . . . child_gene=1;child_mRNA=1
seq04 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1
seq05 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1
@@ -35,48 +35,48 @@ seq06 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1
seq07 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;riil=201
seq07 AEGeAn::LocusPocus locus 801 1001 . . . fg_orient=FF
seq07 AEGeAn::LocusPocus locus 1002 1600 . . . liil=201;child_gene=1;child_mRNA=1
-seq07 AEGeAn::LocusPocus locus 1601 2000 . . . fragment=true
+seq07 AEGeAn::LocusPocus locus 1601 2000 . . . .
seq08 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;riil=200
seq08 AEGeAn::LocusPocus locus 801 1000 . . . fg_orient=FF
seq08 AEGeAn::LocusPocus locus 1001 1600 . . . liil=200;child_gene=1;child_mRNA=1
-seq08 AEGeAn::LocusPocus locus 1601 2000 . . . fragment=true
+seq08 AEGeAn::LocusPocus locus 1601 2000 . . . .
seq09 AEGeAn::LocusPocus locus 1 900 . . . child_gene=1;child_mRNA=1;iiLocus_exception=delta-re-extend;riil=0
seq09 AEGeAn::LocusPocus locus 901 1600 . . . liil=0;child_gene=1;child_mRNA=1
-seq09 AEGeAn::LocusPocus locus 1601 2000 . . . fragment=true
+seq09 AEGeAn::LocusPocus locus 1601 2000 . . . .
seq10 AEGeAn::LocusPocus locus 1 801 . . . child_gene=1;child_mRNA=1;iiLocus_exception=delta-re-extend;riil=0
seq10 AEGeAn::LocusPocus locus 802 1500 . . . liil=0;child_gene=1;child_mRNA=1
-seq10 AEGeAn::LocusPocus locus 1501 2000 . . . fragment=true
+seq10 AEGeAn::LocusPocus locus 1501 2000 . . . .
seq11 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;iiLocus_exception=delta-re-extend;riil=0
seq11 AEGeAn::LocusPocus locus 801 1500 . . . liil=0;child_gene=1;child_mRNA=1
-seq11 AEGeAn::LocusPocus locus 1501 2000 . . . fragment=true
+seq11 AEGeAn::LocusPocus locus 1501 2000 . . . .
seq12 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=1;iiLocus_exception=delta-overlap-delta;riil=0
seq12 AEGeAn::LocusPocus locus 800 1500 . . . left_overlap=1;liil=0;child_gene=1;child_mRNA=1
-seq12 AEGeAn::LocusPocus locus 1501 2000 . . . fragment=true
+seq12 AEGeAn::LocusPocus locus 1501 2000 . . . .
seq13 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=198;iiLocus_exception=delta-overlap-delta;riil=0
seq13 AEGeAn::LocusPocus locus 603 1300 . . . left_overlap=198;liil=0;child_gene=1;child_mRNA=1
-seq13 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
+seq13 AEGeAn::LocusPocus locus 1301 1500 . . . .
seq14 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=199;iiLocus_exception=delta-overlap-delta;riil=0
seq14 AEGeAn::LocusPocus locus 602 1300 . . . left_overlap=199;liil=0;child_gene=1;child_mRNA=1
-seq14 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
+seq14 AEGeAn::LocusPocus locus 1301 1500 . . . .
seq15 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=200;iiLocus_exception=delta-overlap-delta;riil=0
seq15 AEGeAn::LocusPocus locus 601 1300 . . . left_overlap=200;liil=0;child_gene=1;child_mRNA=1
-seq15 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
+seq15 AEGeAn::LocusPocus locus 1301 1500 . . . .
seq16 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=201;iiLocus_exception=delta-overlap-gene;riil=0
seq16 AEGeAn::LocusPocus locus 600 1300 . . . left_overlap=201;liil=0;child_gene=1;child_mRNA=1
-seq16 AEGeAn::LocusPocus locus 1301 1500 . . . fragment=true
+seq16 AEGeAn::LocusPocus locus 1301 1500 . . . .
seq17 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=395;iiLocus_exception=delta-overlap-gene;riil=0
seq17 AEGeAn::LocusPocus locus 406 1200 . . . left_overlap=395;liil=0;child_gene=1;child_mRNA=1
-seq17 AEGeAn::LocusPocus locus 1201 1500 . . . fragment=true
+seq17 AEGeAn::LocusPocus locus 1201 1500 . . . .
seq18 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=399;iiLocus_exception=delta-overlap-gene;riil=0
seq18 AEGeAn::LocusPocus locus 402 1200 . . . left_overlap=399;liil=0;child_gene=1;child_mRNA=1
-seq18 AEGeAn::LocusPocus locus 1201 1500 . . . fragment=true
+seq18 AEGeAn::LocusPocus locus 1201 1500 . . . .
seq19 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1;right_overlap=400;iiLocus_exception=delta-overlap-gene;riil=0
seq19 AEGeAn::LocusPocus locus 401 1200 . . . left_overlap=400;liil=0;child_gene=1;child_mRNA=1
-seq19 AEGeAn::LocusPocus locus 1201 1500 . . . fragment=true
+seq19 AEGeAn::LocusPocus locus 1201 1500 . . . .
seq20 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1
-seq20 AEGeAn::LocusPocus locus 801 1001 . . . fragment=true
+seq20 AEGeAn::LocusPocus locus 801 1001 . . . .
seq21 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1
-seq21 AEGeAn::LocusPocus locus 801 1000 . . . fragment=true
+seq21 AEGeAn::LocusPocus locus 801 1000 . . . .
seq22 AEGeAn::LocusPocus locus 1 999 . . . child_gene=1;child_mRNA=1
seq23 AEGeAn::LocusPocus locus 1 801 . . . child_gene=1;child_mRNA=1
seq24 AEGeAn::LocusPocus locus 1 800 . . . child_gene=1;child_mRNA=1
diff --git a/data/gff3/mrot-cst-out-cds.gff3 b/data/gff3/mrot-cst-out-cds.gff3
index aae711a..957cac8 100644
--- a/data/gff3/mrot-cst-out-cds.gff3
+++ b/data/gff3/mrot-cst-out-cds.gff3
@@ -6,5 +6,5 @@
#!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=piLocus;child_gene=1;child_mRNA=1
-NW_003797177.1 AEGeAn::LocusPocus locus 11405 18146 . . . iiLocus_exception=intron-gene;iLocus_type=piLocus;child_gene=1;child_mRNA=4
+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 11405 18146 . . . iiLocus_exception=intron-gene;iLocus_type=siLocus;child_gene=1;child_mRNA=4
diff --git a/data/gff3/nvit-exospindle-out.gff3 b/data/gff3/nvit-exospindle-out.gff3
index 30da870..b836157 100644
--- a/data/gff3/nvit-exospindle-out.gff3
+++ b/data/gff3/nvit-exospindle-out.gff3
@@ -6,7 +6,7 @@
#!genome-build-accession NCBI_Assembly:GCF_000002325.3
#!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=piLocus
-NC_015867.2 AEGeAn::LocusPocus locus 372891 380536 . . . effective_length=6758;iLocus_type=piLocus;child_gene=1;child_mRNA=1
-NC_015867.2 AEGeAn::LocusPocus locus 374998 378903 . . . iiLocus_exception=intron-gene;iLocus_type=piLocus;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=piLocus
+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 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
diff --git a/data/scripts/miloci.py b/data/scripts/miloci.py
index be6425c..34a32e7 100755
--- a/data/scripts/miloci.py
+++ b/data/scripts/miloci.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-# Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+# Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
#
# The AEGeAn Toolkit is distributed under the ISC License. See
# the 'LICENSE' file in the AEGeAn source code distribution or
@@ -45,7 +45,7 @@ def merge_iloci(loci):
attrs[key] = 0
attrs[key] += value
- attrstring = 'merged=true;iLocus_type=miLocus'
+ attrstring = 'iLocus_type=miLocus'
for key in sorted(attrs):
attrstring += ';%s=%d' % (key, attrs[key])
gff3 = [seqid, 'AEGeAn::miloci.py', 'locus', str(start), str(end),
@@ -82,7 +82,7 @@ def parse_iloci(fp):
if len(prev_loci) > 0:
yield merge_iloci(prev_loci)
prev_loci = []
- line = re.sub('ID=[^;\n]+;*', 'geneless=true;', line)
+ line = re.sub('ID=[^;\n]+;*', '', line)
line = re.sub('Name=[^;\n]+;*', '', line)
yield line
if len(prev_loci) > 0:
diff --git a/data/scripts/uloci.py b/data/scripts/uloci.py
index 1828f09..8d223d1 100755
--- a/data/scripts/uloci.py
+++ b/data/scripts/uloci.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-# Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+# Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
#
# The AEGeAn Toolkit is distributed under the ISC License. See
# the 'LICENSE' file in the AEGeAn source code distribution or
@@ -111,8 +111,8 @@ if __name__ == '__main__':
for seqid, seqlen in parse_gff3(args.infile):
locid = args.idfmt % args.counter
args.counter += 1
- attrs = 'ID=%s;Name=%s;fragment=true;unannot=true;' % (locid, locid)
- attrs += 'iLocus_type=iiLocus;effective_length=%d' % seqlen
+ attrs = 'ID=%s;Name=%s;unannot=true;' % (locid, locid)
+ attrs += 'iLocus_type=fiLocus;effective_length=%d' % seqlen
fields = [seqid, args.src, 'locus', '1', str(seqlen), '.', '.', '.',
attrs]
print(*fields, sep='\t')
diff --git a/docs/contrib.rst b/docs/contrib.rst
index 7888185..161cb5f 100644
--- a/docs/contrib.rst
+++ b/docs/contrib.rst
@@ -4,7 +4,8 @@ The following assisted in the development of the AEGeAn Toolkit and/or
contributed to its code base.
* Daniel S. Standage <daniel.standage at gmail.com>, primary developer
-* Volker Brendel <vbrendel at indiana.edu>, supervision and testing
+* Volker Brendel <vbrendel at indiana.edu>, intellectual development, supervision,
+ and testing
* Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> and Gordon Gremme
<gordon at gremme.org>, integration with GenomeTools, including code examples
and implementing feature requests
diff --git a/src/core/AgnLocus.c b/src/core/AgnLocus.c
index 04b2aa3..20ceb24 100644
--- a/src/core/AgnLocus.c
+++ b/src/core/AgnLocus.c
@@ -344,7 +344,7 @@ void agn_locus_data_aggregate(AgnLocus *locus, AgnComparisonData *data)
break;
default:
desc = NULL;
- fprintf(stderr, "error: unknow comp classification %d\n", c);
+ fprintf(stderr, "error: unknown comp classification %d\n", c);
break;
}
desc->comparison_count++;
diff --git a/src/core/AgnLocusRefineStream.c b/src/core/AgnLocusRefineStream.c
index 0ae0e4d..65d1522 100644
--- a/src/core/AgnLocusRefineStream.c
+++ b/src/core/AgnLocusRefineStream.c
@@ -1,6 +1,6 @@
/**
-Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
The AEGeAn Toolkit is distributed under the ISC License. See
the 'LICENSE' file in the AEGeAn source code distribution or
@@ -182,12 +182,12 @@ bool agn_locus_refine_stream_unit_test(AgnUnitTest *test)
if(elen)
test1a = strcmp(elen, "11466") == 0;
gt_genome_node_delete(locus);
-
+
locus = gt_queue_get(queue);
locusrange = gt_genome_node_get_range(locus);
test1 = test1 && locusrange.start == 1916352 && locusrange.end == 1927323;
gt_genome_node_delete(locus);
-
+
locus = gt_queue_get(queue);
locusrange = gt_genome_node_get_range(locus);
test1 = test1 && locusrange.start == 1918157 && locusrange.end == 1921155;
@@ -211,7 +211,7 @@ bool agn_locus_refine_stream_unit_test(AgnUnitTest *test)
if(elen)
test2a = strcmp(elen, "9660") == 0;
gt_genome_node_delete(locus);
-
+
locus = gt_queue_get(queue);
locusrange = gt_genome_node_get_range(locus);
test2 = test2 && locusrange.start == 11405 && locusrange.end == 18146;
@@ -293,7 +293,7 @@ static bool refine_locus_check_intron_genes(AgnLocusRefineStream *stream,
gt_array_delete(exons);
return false;
}
-
+
GtUword i;
bool overlap = false;
for(i = 0; i < gt_array_size(exons); i++)
@@ -368,7 +368,7 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,
gnrange.end = origrange.end;
else
gnrange.end += stream->delta;
-
+
agn_locus_set_range(*gn, gnrange.start, gnrange.end);
agn_assert(gt_range_contains(&origrange, &gnrange));
gt_feature_node_set_source(fn, stream->source);
@@ -418,7 +418,7 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,
break;
}
}
-
+
// If the iLoci are all coding or all non-coding, just assign their collective
// length (sans overlap from previous unrefined iLocus) to the first refined
// iLocus.
@@ -449,12 +449,12 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,
}
}
}
- const char *typestr = "piLocus";
+ const char *typestr = "siLocus";
if(coding_status == false)
typestr = "niLocus";
else if(agn_locus_num_genes(*gn) > 1)
{
- typestr = "complex";
+ typestr = "ciLocus";
char exceptstr[32];
GtUword genenum = agn_typecheck_count(origfn, agn_typecheck_gene);
@@ -492,13 +492,13 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,
bool cds1 = agn_locus_num_mrnas(*gn1) > 0;
if(cds1 == true)
{
- gt_feature_node_add_attribute(fn1, "iLocus_type", "piLocus");
+ gt_feature_node_add_attribute(fn1, "iLocus_type", "siLocus");
gt_feature_node_add_attribute(fn2, "iLocus_type", "niLocus");
}
else
{
gt_feature_node_add_attribute(fn1, "iLocus_type", "niLocus");
- gt_feature_node_add_attribute(fn2, "iLocus_type", "piLocus");
+ gt_feature_node_add_attribute(fn2, "iLocus_type", "siLocus");
}
const char *exc = gt_feature_node_get_attribute(fn2, "iiLocus_exception");
@@ -524,7 +524,7 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,
gt_feature_node_add_attribute(fn1, "riil", orig_riil);
}
}
-
+
// The genes overlap
else
{
@@ -611,14 +611,18 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,
gt_feature_node_add_attribute(fn, "riil", "0");
}
- const char *type = "complex";
- if(agn_locus_num_genes(*gn) == 1)
+ const char *type = "";
+ if(agn_locus_num_mrnas(*gn) == 0)
{
- if(agn_locus_num_mrnas(*gn) > 0)
- type = "piLocus";
- else
- type = "niLocus";
-
+ type = "niLocus";
+ }
+ else if(agn_locus_num_genes(*gn) == 1)
+ {
+ type = "siLocus";
+ }
+ else
+ {
+ type = "ciLocus";
}
gt_feature_node_add_attribute(fn, "iLocus_type", type);
}
@@ -655,12 +659,20 @@ static int locus_refine_stream_handler(AgnLocusRefineStream *stream,
sprintf(lenstr, "%lu", gt_range_length(&rng) - ro);
gt_feature_node_add_attribute(locus, "effective_length", lenstr);
- if(gt_feature_node_number_of_children(locus) == 0)
- gt_feature_node_add_attribute(locus, "iLocus_type", "iiLocus");
- else if(agn_locus_num_mrnas(gn) > 0)
- gt_feature_node_add_attribute(locus, "iLocus_type", "piLocus");
+ const char *loctype = gt_genome_node_get_user_data(gn, "iLocus_type");
+ if(loctype == NULL)
+ {
+ if(gt_feature_node_number_of_children(locus) == 0)
+ gt_feature_node_add_attribute(locus, "iLocus_type", "iiLocus");
+ else if(agn_locus_num_mrnas(gn) > 0)
+ gt_feature_node_add_attribute(locus, "iLocus_type", "siLocus");
+ else
+ gt_feature_node_add_attribute(locus, "iLocus_type", "niLocus");
+ }
else
- gt_feature_node_add_attribute(locus, "iLocus_type", "niLocus");
+ {
+ gt_feature_node_add_attribute(locus, "iLocus_type", loctype);
+ }
gt_queue_add(stream->locusqueue, locus);
return 0;
}
diff --git a/src/core/AgnLocusStream.c b/src/core/AgnLocusStream.c
index 93ea047..f0f7f1b 100644
--- a/src/core/AgnLocusStream.c
+++ b/src/core/AgnLocusStream.c
@@ -1,6 +1,6 @@
/**
-Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
The AEGeAn Toolkit is distributed under the ISC License. See
the 'LICENSE' file in the AEGeAn source code distribution or
@@ -262,13 +262,12 @@ static void locus_stream_extend(AgnLocusStream *stream, AgnLocus *locus)
locusrange.end);
if(stream->endmode >= 0 && !stream->skip_iiLoci)
{
- AgnLocus *iilocus = agn_locus_new(seqid);
- GtRange irange = { seqrange.start,
- locusrange.start - stream->delta - 1 };
- agn_locus_set_range(iilocus, irange.start, irange.end);
- GtFeatureNode *iilocfn = gt_feature_node_cast(iilocus);
- gt_feature_node_add_attribute(iilocfn, "fragment", "true");
- gt_queue_add(stream->locusqueue, iilocus);
+ AgnLocus *filocus = agn_locus_new(seqid);
+ GtRange irange = {seqrange.start, locusrange.start - stream->delta - 1};
+ agn_locus_set_range(filocus, irange.start, irange.end);
+ gt_genome_node_add_user_data(filocus, "iLocus_type",
+ gt_cstr_dup("fiLocus"), gt_free_func);
+ gt_queue_add(stream->locusqueue, filocus);
}
}
else
@@ -397,12 +396,12 @@ static void locus_stream_extend(AgnLocusStream *stream, AgnLocus *locus)
locusrange.end + stream->delta);
if(stream->endmode >= 0 && !stream->skip_iiLoci)
{
- AgnLocus *term_locus = agn_locus_new(seqid);
- agn_locus_set_range(term_locus,
- locusrange.end + stream->delta + 1, seqrange.end);
- GtFeatureNode *tlfn = (GtFeatureNode *)term_locus;
- gt_feature_node_add_attribute(tlfn, "fragment", "true");
- gt_queue_add(stream->locusqueue, term_locus);
+ AgnLocus *filocus = agn_locus_new(seqid);
+ GtRange irange = {locusrange.end + stream->delta + 1, seqrange.end};
+ agn_locus_set_range(filocus, irange.start, irange.end);
+ gt_genome_node_add_user_data(filocus, "iLocus_type",
+ gt_cstr_dup("fiLocus"), gt_free_func);
+ gt_queue_add(stream->locusqueue, filocus);
}
}
else
@@ -863,4 +862,3 @@ static void locus_stream_unit_test_loci(AgnUnitTest *test)
gt_queue_delete(queue);
}
-
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aegean.git
More information about the debian-med-commit
mailing list