Fix some issues in gcc9

Description: Fix some issues in gcc-9

Author: Andreas Tille <tille@debian.org>

Last-Update: Thu, 19 Dec 2019 08:14:41 +0100

--- a/src/main/ccs.cpp

+++ b/src/main/ccs.cpp

@@ -10,6 +10,7 @@

 #include <sstream>

 #include <string>

 #include <vector>

+#include <iomanip>

 #include <boost/algorithm/string.hpp>

 #include <boost/algorithm/string/join.hpp>

@@ -468,7 +469,7 @@ static int Runner(const PacBio::CLI::Res

             std::make_unique<BamWriter>(outputFile, PrepareHeader(args.InputCommandLine(), ds));

         const string pbiFileName = outputFile + ".pbi";

         auto ccsPbi = std::make_unique<PbiBuilder>(pbiFileName);

-        writer = async(launch::async, BamWriterThread, ref(workQueue), move(ccsBam), move(ccsPbi),

+        writer = async(launch::async, BamWriterThread, ref(workQueue), std::move(ccsBam), move(ccsPbi),

                        settings);

         // Always generate pbi file

@@ -567,8 +568,8 @@ static int Runner(const PacBio::CLI::Res

         chunk->back().Reads.emplace_back(

             Subread{ReadId(movieNames[movieName], *holeNumber,

                            Interval(read.QueryStart(), read.QueryEnd())),

-                    read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),

-                    read.ReadAccuracy(), SNR(read.SignalToNoise()), move(chem)});

+                    read.Sequence(), std::move(ipd), std::move(pw), read.LocalContextFlags(),

+                    read.ReadAccuracy(), SNR(read.SignalToNoise()), std::move(chem)});

     }

     // run the remaining tasks

no-static-linking.patch

do_not_refer_to_non-existing_images.patch

2to3.patch

gcc9.patch