[med-svn] [Git][med-team/freebayes][master] 2 commits: match bedreader interface to new intervaltree
Andreas Tille
gitlab at salsa.debian.org
Thu Dec 19 13:14:00 GMT 2019
Andreas Tille pushed to branch master at Debian Med / freebayes
Commits:
36e0b3c7 by Andreas Tille at 2019-12-19T11:51:10Z
match bedreader interface to new intervaltree
- - - - -
fc417bc9 by Andreas Tille at 2019-12-19T12:43:55Z
Another Python3 fix
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6.patch
- debian/patches/series
- debian/patches/vcffirstheader.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -9,10 +9,17 @@ freebayes (1.3.2-1) UNRELEASED; urgency=medium
* Remove trailing whitespace in debian/copyright
* Set upstream metadata fields: Repository, Repository-Browse.
* Versioned Build-Depends: libseqlib-dev (>= 1.1.2+dfsg-5)
- TODO: Does not build with Debian packaged libs. Opened upstream issue
- https://github.com/ekg/freebayes/issues/579
-
- -- Andreas Tille <tille at debian.org> Tue, 17 Dec 2019 10:46:24 +0100
+ TODO:
+ t/01_call_variants.t ...............
+ 1..23
+ ...
+ not ok 16 - running in parallel makes no difference
+ # got: '154'
+ # expected: '0'
+ ...
+ Failed 1/23 subtests
+
+ -- Andreas Tille <tille at debian.org> Thu, 19 Dec 2019 12:51:28 +0100
freebayes (1.3.1-1) unstable; urgency=medium
=====================================
debian/patches/1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6.patch
=====================================
@@ -0,0 +1,101 @@
+From 1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6 Mon Sep 17 00:00:00 2001
+From: Erik Garrison <erik.garrison at gmail.com>
+Date: Thu, 19 Dec 2019 11:03:01 +0100
+Subject: [PATCH] match bedreader interface to new intervaltree
+Origin: https://github.com/ekg/freebayes/pull/581/commits/1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6
+
+---
+ src/BedReader.cpp | 16 ++++++----------
+ src/BedReader.h | 10 +++++-----
+ src/Fasta.cpp | 4 ++--
+ 3 files changed, 14 insertions(+), 18 deletions(-)
+
+--- a/src/BedReader.cpp
++++ b/src/BedReader.cpp
+@@ -46,32 +46,28 @@ vector<BedTarget> BedReader::entries(voi
+ }
+
+ bool BedReader::targetsContained(string& seq, long left, long right) {
+- vector<Interval<BedTarget*> > results;
+- intervals[seq].findContained(left, right, results);
++ vector<Interval<int, BedTarget*> > results = intervals[seq].findContained(left, right);
+ return !results.empty();
+ }
+
+ bool BedReader::targetsOverlap(string& seq, long left, long right) {
+- vector<Interval<BedTarget*> > results;
+- intervals[seq].findOverlapping(left, right, results);
++ vector<Interval<int, BedTarget*> > results = intervals[seq].findOverlapping(left, right);
+ return !results.empty();
+ }
+
+ vector<BedTarget*> BedReader::targetsContaining(BedTarget& target) {
+- vector<Interval<BedTarget*> > results;
+- intervals[target.seq].findContained(target.left, target.right, results);
++ vector<Interval<int, BedTarget*> > results = intervals[target.seq].findContained(target.left, target.right);
+ vector<BedTarget*> contained;
+- for (vector<Interval<BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
++ for (vector<Interval<int, BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
+ contained.push_back(r->value);
+ }
+ return contained;
+ }
+
+ vector<BedTarget*> BedReader::targetsOverlapping(BedTarget& target) {
+- vector<Interval<BedTarget*> > results;
+- intervals[target.seq].findOverlapping(target.left, target.right, results);
++ vector<Interval<int, BedTarget*> > results = intervals[target.seq].findOverlapping(target.left, target.right);
+ vector<BedTarget*> overlapping;
+- for (vector<Interval<BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
++ for (vector<Interval<int, BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
+ overlapping.push_back(r->value);
+ }
+ return overlapping;
+--- a/src/BedReader.h
++++ b/src/BedReader.h
+@@ -38,7 +38,7 @@ class BedReader : public ifstream {
+
+ public:
+ vector<BedTarget> targets;
+- map<string, IntervalTree<BedTarget*> > intervals; // intervals by reference sequence
++ map<string, IntervalTree<int, BedTarget*> > intervals; // intervals by reference sequence
+
+ vector<BedTarget> entries(void);
+
+@@ -60,12 +60,12 @@ public:
+ }
+
+ void buildIntervals(void) {
+- map<string, vector<Interval<BedTarget*> > > intervalsBySeq;
++ map<string, IntervalTree<int, BedTarget*>::interval_vector> intervalsBySeq;
+ for (vector<BedTarget>::iterator t = targets.begin(); t != targets.end(); ++t) {
+- intervalsBySeq[t->seq].push_back(Interval<BedTarget*>(t->left, t->right, &*t));
++ intervalsBySeq[t->seq].push_back(Interval<int, BedTarget*>(t->left, t->right, &*t));
+ }
+- for (map<string, vector<Interval<BedTarget*> > >::iterator s = intervalsBySeq.begin(); s != intervalsBySeq.end(); ++s) {
+- intervals[s->first] = IntervalTree<BedTarget*>(s->second);
++ for (map<string, IntervalTree<int, BedTarget*>::interval_vector>::const_iterator s = intervalsBySeq.begin(); s != intervalsBySeq.end(); ++s) {
++ intervals[s->first] = IntervalTree<int, BedTarget*>((IntervalTree<int, BedTarget*>::interval_vector&&)s->second);
+ }
+ }
+
+--- a/src/Fasta.cpp
++++ b/src/Fasta.cpp
+@@ -262,7 +262,7 @@ string FastaReference::getRawSequence(st
+ int seqlen = newlines_in_sequence + entry.length;
+ char* seq = (char*) calloc (seqlen + 1, sizeof(char));
+ fseek64(file, entry.offset, SEEK_SET);
+- fread(seq, sizeof(char), seqlen, file);
++ size_t x = fread(seq, sizeof(char), seqlen, file);
+ seq[seqlen] = '\0';
+ char* pbegin = seq;
+ char* pend = seq + (seqlen/sizeof(char));
+@@ -305,7 +305,7 @@ string FastaReference::getRawSubSequence
+ int seqlen = length + newlines_inside;
+ char* seq = (char*) calloc (seqlen + 1, sizeof(char));
+ fseek64(file, (off_t) (entry.offset + newlines_before + start), SEEK_SET);
+- fread(seq, sizeof(char), (off_t) seqlen, file);
++ size_t x = fread(seq, sizeof(char), (off_t) seqlen, file);
+ seq[seqlen] = '\0';
+ char* pbegin = seq;
+ char* pend = seq + (seqlen/sizeof(char));
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ fix_test.patch
vcffirstheader.patch
skip_failing_test.patch
2to3.patch
+1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6.patch
=====================================
debian/patches/vcffirstheader.patch
=====================================
@@ -11,7 +11,7 @@ Description: This script was not part of the vcflib release
--- /dev/null
+++ b/vcflib/scripts/vcffirstheader
@@ -0,0 +1,16 @@
-+#!/usr/bin/env python
++#!/usr/bin/python3
+
+import sys
+
@@ -19,11 +19,11 @@ Description: This script was not part of the vcflib release
+for line in sys.stdin:
+ if line.startswith('##'):
+ if header:
-+ print line.strip()
++ print(line.strip())
+ continue
+ elif line.startswith('#'):
+ if header:
-+ print line.strip()
++ print(line.strip())
+ header=False
+ continue
-+ print line.strip()
++ print(line.strip())
View it on GitLab: https://salsa.debian.org/med-team/freebayes/compare/6a92209981ebf43bad7a0a18dada4c83bf5a1a45...fc417bc9b1270fb0c6887fcc883d3b34b163e91a
--
View it on GitLab: https://salsa.debian.org/med-team/freebayes/compare/6a92209981ebf43bad7a0a18dada4c83bf5a1a45...fc417bc9b1270fb0c6887fcc883d3b34b163e91a
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