debian/control

@@ -5,6 +5,7 @@ Uploaders: Michael R. Crusoe <michael.crusoe@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

+Author: Andreas Tille <tille@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/