[med-svn] [Git][med-team/sga][debian/unstable] 3 commits: Fix some build issues with gcc9
Andreas Tille
gitlab at salsa.debian.org
Sun Dec 22 17:58:37 GMT 2019
Andreas Tille pushed to branch debian/unstable at Debian Med / sga
Commits:
feaf2ad1 by Andreas Tille at 2019-12-22T17:42:51Z
Fix some build issues with gcc9
- - - - -
43bbd4cf by Andreas Tille at 2019-12-22T17:47:47Z
More Python3 changes
- - - - -
f37b7a57 by Andreas Tille at 2019-12-22T17:58:04Z
Fix Python3 dependency
- - - - -
5 changed files:
- debian/control
- debian/patches/2to3.patch
- + debian/patches/gcc9.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -5,6 +5,7 @@ Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
+ dh-python,
libsparsehash-dev,
zlib1g-dev | libz-dev,
libbamtools-dev,
@@ -24,9 +25,9 @@ Homepage: https://github.com/jts/sga
Package: sga
Architecture: any
Depends: ${shlibs:Depends},
+ ${python3:Depends},
${misc:Depends},
samtools,
- python3,
python3-ruffus,
python3-pysam
Recommends: abyss (>= 2.0.2-1)
=====================================
debian/patches/2to3.patch
=====================================
@@ -93,3 +93,197 @@ Last-Update: Mon, 02 Sep 2019 20:18:33 +0200
marker = d['plot_marker'] if( use_markers ) else None
ax.plot(indices, q30_fraction, '-',
marker=marker, color=d['plot_color'])
+--- a/src/bin/sga-joinedpe
++++ b/src/bin/sga-joinedpe
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+ # sga-joinpe - join the two ends of a paired end read together
+ # into one composite sequence. This is used to run rmdup on the pairs
+ import getopt
+@@ -9,7 +9,7 @@ def writeJoinedRecord(out, record1, reco
+ join_name_1 = record1[0].split()[0][0:-2]
+ join_name_2 = record2[0].split()[0][0:-2]
+ if join_name_1 != join_name_2:
+- print 'Error: Reads are incorrectly paired ', record1[0], record2[0]
++ print('Error: Reads are incorrectly paired ', record1[0], record2[0])
+ sys.exit(2)
+
+ join_pos = len(record1[1])
+@@ -30,7 +30,7 @@ def writeSplitRecord(out, record):
+ if header_fields[1].find("join_pos") != -1:
+ join_pos = int(header_fields[1].split(":")[1])
+ else:
+- print 'Error: joined record does not have the correct format ', record[0]
++ print('Error: joined record does not have the correct format ', record[0])
+
+ # print 'join_pos', join_pos
+ id1 = header_fields[0] + "/1"
+@@ -76,7 +76,7 @@ def readRecord(file):
+ elif id[0] == "@":
+ isFastq = True
+ else:
+- print 'Unknown record header: ', line
++ print('Unknown record header: ', line)
+ sys.exit(2)
+
+ out.append(id)
+@@ -90,15 +90,15 @@ def readRecord(file):
+
+ #
+ def usage():
+- print 'sga-joinedpe [-o outfile] FILE'
+- print 'allow rmdup to be performed on entire paired end reads'
+- print 'if the --join option is provided, two consequetive records in FILE will be concatenated into one read.'
+- print 'if the --split option is provided, each record in FILE will be split into two'
+- print '\nOptions: '
+- print ' -o, --outfile=FILE Write results to FILE [default=stdout]'
+- print ' --join Join the reads together'
+- print ' --split Split the reads apart'
+- print ' --help Print this usage message'
++ print('sga-joinedpe [-o outfile] FILE')
++ print('allow rmdup to be performed on entire paired end reads')
++ print('if the --join option is provided, two consequetive records in FILE will be concatenated into one read.')
++ print('if the --split option is provided, each record in FILE will be split into two')
++ print('\nOptions: ')
++ print(' -o, --outfile=FILE Write results to FILE [default=stdout]')
++ print(' --join Join the reads together')
++ print(' --split Split the reads apart')
++ print(' --help Print this usage message')
+
+ # Defaults
+ outfilename = ""
+@@ -111,8 +111,8 @@ try:
+ "split",
+ "join",
+ "help"])
+-except getopt.GetoptError, err:
+- print str(err)
++except getopt.GetoptError as err:
++ print(str(err))
+ usage()
+ sys.exit(2)
+
+@@ -127,20 +127,20 @@ for (oflag, oarg) in opts:
+ usage()
+ sys.exit(1)
+ else:
+- print 'Unrecognized argument', oflag
++ print('Unrecognized argument', oflag)
+ usage()
+ sys.exit(0)
+
+ if len(args) != 1:
+- print 'Error: Exactly one input file must be provided'
++ print('Error: Exactly one input file must be provided')
+ sys.exit(2)
+
+ if not join and not split:
+- print 'Error: One of --join or --split must be provided'
++ print('Error: One of --join or --split must be provided')
+ sys.exit(2)
+
+ if join and split:
+- print 'Error: Only one of --join or --split can be provided'
++ print('Error: Only one of --join or --split can be provided')
+ sys.exit(2)
+
+ filename = args[0]
+@@ -158,7 +158,7 @@ if join:
+ record2 = readRecord(file)
+
+ if len(record1) != len(record2):
+- print 'Error, record lengths differ'
++ print('Error, record lengths differ')
+ sys.exit(2)
+
+ # If no record was read, we are done
+--- a/src/bin/sga-align
++++ b/src/bin/sga-align
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+
+ # pipeline to align reads to contigs implemented with ruffus (http://ruffus.org.uk)
+ from ruffus import *
+@@ -14,7 +14,7 @@ def getBasename(inFile):
+
+ # Run a shell command
+ def runCmd(cmd):
+- print cmd
++ print(cmd)
+ return subprocess.Popen(cmd, shell=True).wait()
+
+ def _align(ref, reads, out):
+@@ -29,11 +29,11 @@ def runBWAIndex(inFile):
+ def runBWAAln(inFiles, contigsFile, outFile):
+ assert len(inFiles) == 2
+ if inFiles[0] == inFiles[1]:
+- print 'Error: the two reads files are the same'
++ print('Error: the two reads files are the same')
+ sys.exit(1)
+
+ contigsBasename = getBasename(contigsFile)
+- tempSAI = map(lambda x : getBasename(x) + "." + contigsBasename + ".bwsai", inFiles)
++ tempSAI = [getBasename(x) + "." + contigsBasename + ".bwsai" for x in inFiles]
+
+ _align(contigsFile, inFiles[0], tempSAI[0])
+ _align(contigsFile, inFiles[1], tempSAI[1])
+@@ -65,11 +65,11 @@ def runSplitReads(inFiles, outFiles):
+
+ #
+ def usage():
+- print 'usage: sga-align [options] <contigs file> <input files>'
+- print 'align reads to contigs'
+- print 'Options:'
+- print ' --name=STR Use STR as the basename for the output files.'
+- print ' -t,--threads=N Use N threads when running bwa.'
++ print('usage: sga-align [options] <contigs file> <input files>')
++ print('align reads to contigs')
++ print('Options:')
++ print(' --name=STR Use STR as the basename for the output files.')
++ print(' -t,--threads=N Use N threads when running bwa.')
+
+
+ # Variables
+@@ -79,8 +79,8 @@ try:
+ opts, args = getopt.gnu_getopt(sys.argv[1:], 't:', ["name=",
+ "threads=",
+ "help"])
+-except getopt.GetoptError, err:
+- print str(err)
++except getopt.GetoptError as err:
++ print(str(err))
+ usage()
+ sys.exit(2)
+
+@@ -93,12 +93,12 @@ for (oflag, oarg) in opts:
+ usage()
+ sys.exit(1)
+ else:
+- print 'Unrecognized argument', oflag
++ print('Unrecognized argument', oflag)
+ usage()
+ sys.exit(0)
+
+ if len(args) < 2:
+- print 'Error, a contigs file and reads file must be provided'
++ print('Error, a contigs file and reads file must be provided')
+ usage()
+ sys.exit(0)
+
+@@ -107,11 +107,11 @@ contigFile = args[0]
+ readFiles = args[1:]
+
+ if len(readFiles) == 0:
+- print 'Error, at least one input file must be specified'
++ print('Error, at least one input file must be specified')
+ sys.exit(0)
+
+-print contigFile
+-print readFiles
++print(contigFile)
++print(readFiles)
+
+ indexInFiles = contigFile
+ indexOutFiles = [contigFile + ".bwt"]
=====================================
debian/patches/gcc9.patch
=====================================
@@ -0,0 +1,37 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 22 Dec 2019 18:42:14 +0100
+Description: Fix some build issues with gcc9
+
+--- a/src/Util/ClusterReader.cpp
++++ b/src/Util/ClusterReader.cpp
+@@ -67,7 +67,7 @@ bool ClusterReader::generate(ClusterVect
+ bool ClusterReader::readCluster(ClusterRecord& record)
+ {
+ std::string line;
+- bool good = getline(*m_pReader, line);
++ bool good = (bool)getline(*m_pReader, line);
+ if(!good || line.empty())
+ return false;
+ std::stringstream parser(line);
+--- a/src/Util/StdAlnTools.cpp
++++ b/src/Util/StdAlnTools.cpp
+@@ -119,7 +119,7 @@ std::string StdAlnTools::expandCigar(con
+ char code;
+ while(parser >> length)
+ {
+- bool success = parser >> code;
++ bool success = (bool)(parser >> code);
+ expanded.append(length, code);
+ assert(success);
+ (void)success;
+--- a/src/SGA/rmdup.cpp
++++ b/src/SGA/rmdup.cpp
+@@ -232,7 +232,7 @@ std::string parseDupHits(const StringVec
+ while(!done)
+ {
+ // Parse a line from the current file
+- bool valid = getline(*reader_vec[currReaderIdx], line);
++ bool valid = (bool)getline(*reader_vec[currReaderIdx], line);
+ ++numRead;
+ // Deal with switching the active reader and the end of files
+ if(!valid || numRead == buffer_size)
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ gcc-7.patch
no_privacy_breach_url.patch
2to3.patch
no_enforcing_c++98.patch
+gcc9.patch
=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
include /usr/share/dpkg/default.mk
%:
- dh $@ --sourcedirectory=src
+ dh $@ --with python3 --sourcedirectory=src
override_dh_auto_configure:
dh_auto_configure -- --with-bamtools=/usr/
View it on GitLab: https://salsa.debian.org/med-team/sga/compare/c28a6bf45e34c5bffbaef99d04a39c87bb556e63...f37b7a575d67f9ca01f9d48ed89e4d2a987bd8e3
--
View it on GitLab: https://salsa.debian.org/med-team/sga/compare/c28a6bf45e34c5bffbaef99d04a39c87bb556e63...f37b7a575d67f9ca01f9d48ed89e4d2a987bd8e3
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