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Qt 5.15 switch before Qt 6 switch #643

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merged 5 commits into from
Feb 20, 2025
Merged

Qt 5.15 switch before Qt 6 switch #643

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927b790
Refactoring for Qt 5.15 switch
ubuntolog Feb 7, 2025
5cb0588
Merge branch 'master' into qt6_switch
ubuntolog Feb 19, 2025
c154634
Refactored tools for Qt 5.15
ubuntolog Feb 19, 2025
fe4d524
Merge branch 'master' into qt6_switch
ubuntolog Feb 20, 2025
296bd62
GSvar: resolved conflicts after merge
ubuntolog Feb 20, 2025
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4 changes: 2 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -111,10 +111,10 @@ clean:
find bin -type f -or -type l | grep -v ".ini" | grep -v "GSvar_" | grep -v "libhts" | xargs -l1 rm -rf

test_lib:
cd bin && ./cppCORE-TEST && ./cppNGS-TEST && ./cppNGSD-TEST && ./cppREST-TEST
cd bin && ./cppCORE-TEST && ./cppXML-TEST && ./cppNGS-TEST && ./cppNGSD-TEST && ./cppREST-TEST

test_lib_windows:
cd bin && ./cppCORE-TEST.exe && ./cppNGS-TEST.exe && ./cppNGSD-TEST.exe && ./cppREST-TEST.exe
cd bin && ./cppCORE-TEST.exe && ./cppXML-TEST.exe && ./cppNGS-TEST.exe && ./cppNGSD-TEST.exe && ./cppREST-TEST.exe

test_server:
cd bin && ./GSvarServer-TEST
Expand Down
9 changes: 4 additions & 5 deletions src/BamCleanHaloplex/main.cpp
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Expand Up @@ -55,8 +55,7 @@ class ConcreteTool
{
++c_reads_failed;
al.setIsUnmapped(true);
al.setIsSecondaryAlignment(true);
//QTextStream(stdout) << "REMOVED: " << al.name() << " " << reader.chromosome(al.chromosomeID()).str() << ":" << al.start() << "-" << al.end() << endl;
al.setIsSecondaryAlignment(true);
}
}

Expand All @@ -65,9 +64,9 @@ class ConcreteTool

//statistics output
QTextStream out(stdout);
out << "overall reads: " << c_reads << endl;
out << "mapped reads : " << c_reads_mapped << " (" << QString::number(100.0*c_reads_mapped/c_reads, 'f', 2) << "%)" << endl;
out << "removed reads: " << c_reads_failed << " (" << QString::number(100.0*c_reads_failed/c_reads, 'f', 2) << "%)" << endl;
out << "overall reads: " << c_reads << QT_ENDL;
out << "mapped reads : " << c_reads_mapped << " (" << QString::number(100.0*c_reads_mapped/c_reads, 'f', 2) << "%)" << QT_ENDL;
out << "removed reads: " << c_reads_failed << " (" << QString::number(100.0*c_reads_failed/c_reads, 'f', 2) << "%)" << QT_ENDL;
}

};
Expand Down
66 changes: 33 additions & 33 deletions src/BamClipOverlap/main.cpp
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Expand Up @@ -210,16 +210,16 @@ class ConcreteTool
}

//verbose mode
if(verbose) out << "forward read: name - " << forward_read.name() << ", region - " << reader.chromosome(forward_read.chromosomeID()).str() << ":" << (forward_read.start()-1) << "-" << forward_read.end() << ", insert size: " << forward_read.insertSize() << " bp; mate: " << forward_read.mateStart() << ", CIGAR " << forward_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << endl;
if(verbose) out << "reverse read: name - " << reverse_read.name() << ", region - " << reader.chromosome(reverse_read.chromosomeID()).str() << ":" << (reverse_read.start()-1) << "-" << reverse_read.end() << ", insert size: " << reverse_read.insertSize() << " bp; mate: " << reverse_read.mateStart() << ", CIGAR " << reverse_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << endl;
if(verbose) out << "forward read bases " << forward_read.bases() << endl;
if(verbose) out << "forward read qualities " << forward_read.qualities() << endl;
if(verbose) out << "forward CIGAR " << forward_read.cigarDataAsString(true) << endl;
if(verbose) out << "reverse read bases " << reverse_read.bases() << endl;
if(verbose) out << "reverse read qualities " << reverse_read.qualities() << endl;
if(verbose) out << "reverse CIGAR " << reverse_read.cigarDataAsString(true) << endl;
if(verbose) out << " clip forward read from position " << (forward_read.end()-clip_forward_read+1) << " to " << forward_read.end() << endl;
if(verbose) out << " clip reverse read from position " << reverse_read.start() << " to " << (reverse_read.start()-1+clip_reverse_read) << endl;
if(verbose) out << "forward read: name - " << forward_read.name() << ", region - " << reader.chromosome(forward_read.chromosomeID()).str() << ":" << (forward_read.start()-1) << "-" << forward_read.end() << ", insert size: " << forward_read.insertSize() << " bp; mate: " << forward_read.mateStart() << ", CIGAR " << forward_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << QT_ENDL;
if(verbose) out << "reverse read: name - " << reverse_read.name() << ", region - " << reader.chromosome(reverse_read.chromosomeID()).str() << ":" << (reverse_read.start()-1) << "-" << reverse_read.end() << ", insert size: " << reverse_read.insertSize() << " bp; mate: " << reverse_read.mateStart() << ", CIGAR " << reverse_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << QT_ENDL;
if(verbose) out << "forward read bases " << forward_read.bases() << QT_ENDL;
if(verbose) out << "forward read qualities " << forward_read.qualities() << QT_ENDL;
if(verbose) out << "forward CIGAR " << forward_read.cigarDataAsString(true) << QT_ENDL;
if(verbose) out << "reverse read bases " << reverse_read.bases() << QT_ENDL;
if(verbose) out << "reverse read qualities " << reverse_read.qualities() << QT_ENDL;
if(verbose) out << "reverse CIGAR " << reverse_read.cigarDataAsString(true) << QT_ENDL;
if(verbose) out << " clip forward read from position " << (forward_read.end()-clip_forward_read+1) << " to " << forward_read.end() << QT_ENDL;
if(verbose) out << " clip reverse read from position " << reverse_read.start() << " to " << (reverse_read.start()-1+clip_reverse_read) << QT_ENDL;

struct Overlap
{
Expand Down Expand Up @@ -275,7 +275,7 @@ class ConcreteTool
};

//check if bases in overlap match
if(verbose) out << " overlap found from " << QString::number(overlap_start) << " to " << QString::number(overlap_end) << endl;
if(verbose) out << " overlap found from " << QString::number(overlap_start) << " to " << QString::number(overlap_end) << QT_ENDL;

//
bool has_indel = false; //INDEL ist around the clipping position
Expand Down Expand Up @@ -327,8 +327,8 @@ class ConcreteTool
THROW(Exception, QByteArray("Unknown CIGAR character '") + forward_cigar[i] + "'")
}
}
if(verbose) out << " finished reading overlap forward bases " << forward_overlap.getBases() << endl;
if(verbose) out << " finished reading overlap forward cigar " << forward_overlap.getCigar() << endl;
if(verbose) out << " finished reading overlap forward bases " << forward_overlap.getBases() << QT_ENDL;
if(verbose) out << " finished reading overlap forward cigar " << forward_overlap.getCigar() << QT_ENDL;

genome_pos = reverse_read.start()-1;
read_pos = 0;
Expand Down Expand Up @@ -375,8 +375,8 @@ class ConcreteTool
THROW(Exception, QByteArray("Unknown CIGAR character '") + reverse_cigar[i] + "'");
}
}
if(verbose) out << " finished reading overlap reverse bases " << reverse_overlap.getBases() << endl;
if(verbose) out << " finished reading overlap reverse cigar " << reverse_overlap.getCigar() << endl;
if(verbose) out << " finished reading overlap reverse bases " << reverse_overlap.getBases() << QT_ENDL;
if(verbose) out << " finished reading overlap reverse cigar " << reverse_overlap.getCigar() << QT_ENDL;

//correct for insertions
for(int i=0;i<forward_overlap.length();++i)
Expand All @@ -391,10 +391,10 @@ class ConcreteTool
forward_overlap.insert(i, '+', 'I', '0', forward_overlap.genome_pos[i], forward_overlap.read_pos[i]);
}
}
if(verbose) out << " finished indel correction forward bases " << forward_overlap.getBases() << endl;
if(verbose) out << " finished indel correction forward cigar " << forward_overlap.getCigar() << endl;
if(verbose) out << " finished indel correction reverse bases " << reverse_overlap.getBases() << endl;
if(verbose) out << " finished indel correction reverse cigar " << reverse_overlap.getCigar() << endl;
if(verbose) out << " finished indel correction forward bases " << forward_overlap.getBases() << QT_ENDL;
if(verbose) out << " finished indel correction forward cigar " << forward_overlap.getCigar() << QT_ENDL;
if(verbose) out << " finished indel correction reverse bases " << reverse_overlap.getBases() << QT_ENDL;
if(verbose) out << " finished indel correction reverse cigar " << reverse_overlap.getCigar() << QT_ENDL;
if(forward_overlap.length()!=reverse_overlap.length()) //both cigar and base string should now be equally long
{
THROW(Exception, "Length mismatch between forward/reverse overlap - forward:" + QByteArray::number(forward_overlap.length()) + " reverse:" + QByteArray::number(reverse_overlap.length()) + " in read with name '" + al.name() + "'");
Expand All @@ -416,7 +416,7 @@ class ConcreteTool

if(verbose && !mm_pos.isEmpty())
{
out << " overlap mismatch for read pair " << forward_read.name() << " - " << forward_overlap.getBases() << " != " << reverse_overlap.getBases() << "!" << endl;
out << " overlap mismatch for read pair " << forward_read.name() << " - " << forward_overlap.getBases() << " != " << reverse_overlap.getBases() << "!" << QT_ENDL;
}

bool map = getFlag("overlap_mismatch_mapq");
Expand All @@ -430,13 +430,13 @@ class ConcreteTool
forward_read.setMappingQuality(0);
reverse_read.setMappingQuality(0);
reads_mismatch += 2;
if(verbose) out << " Set mapping quality to 0." << endl;
if(verbose) out << " Set mapping quality to 0." << QT_ENDL;
}
else if(!mm_pos.isEmpty() && rem)
{
reads_mismatch += 2;
skip_al = true;
if(verbose) out << " Removed pair." << endl;
if(verbose) out << " Removed pair." << QT_ENDL;
}
else if(!mm_pos.isEmpty() && base)
{
Expand All @@ -454,8 +454,8 @@ class ConcreteTool
}
forward_read.setQualities(new_for);
reverse_read.setQualities(new_rev);
if(verbose) out << " changed forward base qualities from " << orig_for << " to " << forward_read.qualities() << endl;
if(verbose) out << " changed reverse base qualities from " << orig_rev << " to " << reverse_read.qualities() << endl;
if(verbose) out << " changed forward base qualities from " << orig_for << " to " << forward_read.qualities() << QT_ENDL;
if(verbose) out << " changed reverse base qualities from " << orig_rev << " to " << reverse_read.qualities() << QT_ENDL;
}
else if(!mm_pos.isEmpty() && basen)
{
Expand All @@ -473,12 +473,12 @@ class ConcreteTool
}
forward_read.setBases(new_for);
reverse_read.setBases(new_rev);
if(verbose) out << " changed forward sequences from " << orig_for << " to " << forward_read.bases() << endl;
if(verbose) out << " changed reverse sequences from " << orig_rev << " to " << reverse_read.bases() << endl;
if(verbose) out << " changed forward sequences from " << orig_for << " to " << forward_read.bases() << QT_ENDL;
if(verbose) out << " changed reverse sequences from " << orig_rev << " to " << reverse_read.bases() << QT_ENDL;
}
else
{
if(verbose) out << " no overlap mismatch for read pair " << forward_read.name() << endl;
if(verbose) out << " no overlap mismatch for read pair " << forward_read.name() << QT_ENDL;
}
}

Expand Down Expand Up @@ -524,9 +524,9 @@ class ConcreteTool
reverse_read.setInsertSize(reverse_insert_size); //negative value
reverse_read.setMateStart(forward_read.start());

if(verbose) out << " clipped forward read: name - " << forward_read.name() << ", region - " << reader.chromosome(forward_read.chromosomeID()).str() << ":" << (forward_read.start()-1) << "-" << forward_end << ", insert size: " << forward_read.insertSize() << " bp; mate: " << forward_read.mateStart() << ", CIGAR " << forward_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << endl;
if(verbose) out << " clipped reverse read: name - " << reverse_read.name() << ", region - " << reader.chromosome(reverse_read.chromosomeID()).str() << ":" << (reverse_read.start()-1) << "-" << reverse_end << ", insert size: " << reverse_read.insertSize() << " bp; mate: " << reverse_read.mateStart() << ", CIGAR " << reverse_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << endl;
if(verbose) out << endl;
if(verbose) out << " clipped forward read: name - " << forward_read.name() << ", region - " << reader.chromosome(forward_read.chromosomeID()).str() << ":" << (forward_read.start()-1) << "-" << forward_end << ", insert size: " << forward_read.insertSize() << " bp; mate: " << forward_read.mateStart() << ", CIGAR " << forward_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << QT_ENDL;
if(verbose) out << " clipped reverse read: name - " << reverse_read.name() << ", region - " << reader.chromosome(reverse_read.chromosomeID()).str() << ":" << (reverse_read.start()-1) << "-" << reverse_end << ", insert size: " << reverse_read.insertSize() << " bp; mate: " << reverse_read.mateStart() << ", CIGAR " << reverse_read.cigarDataAsString() << ", overlap: " << overlap << " bp" << QT_ENDL;
if(verbose) out << QT_ENDL;

//return reads
bases_clipped += overlap;
Expand Down Expand Up @@ -555,9 +555,9 @@ class ConcreteTool

//step 4: write out statistics
if(reads_saved!=reads_count) THROW(ToolFailedException, "Lost Reads: "+QString::number(reads_count-reads_saved)+"/"+QString::number(reads_count));
out << "Overlap mismatch filtering was used for " << QString::number(reads_mismatch) << " of " << QString::number(reads_count) << " reads (" << QString::number((double)reads_mismatch/(double)reads_count*100,'f',2) << " %)." << endl;
out << "Softclipped " << QString::number(reads_clipped) << " of " << QString::number(reads_count) << " reads (" << QString::number(((double)reads_clipped/(double)reads_count*100),'f',2) << " %)." << endl;
out << "Softclipped " << QString::number(bases_clipped) << " of " << QString::number(bases_count) << " basepairs (" << QString::number((double)bases_clipped/(double)bases_count*100,'f',2) << " %)." << endl;
out << "Overlap mismatch filtering was used for " << QString::number(reads_mismatch) << " of " << QString::number(reads_count) << " reads (" << QString::number((double)reads_mismatch/(double)reads_count*100,'f',2) << " %)." << QT_ENDL;
out << "Softclipped " << QString::number(reads_clipped) << " of " << QString::number(reads_count) << " reads (" << QString::number(((double)reads_clipped/(double)reads_count*100),'f',2) << " %)." << QT_ENDL;
out << "Softclipped " << QString::number(bases_clipped) << " of " << QString::number(bases_count) << " basepairs (" << QString::number((double)bases_clipped/(double)bases_count*100,'f',2) << " %)." << QT_ENDL;
}

};
Expand Down
14 changes: 7 additions & 7 deletions src/BamDownsample/main.cpp
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Expand Up @@ -63,7 +63,7 @@ class ConcreteTool
{
++c_se_pass;
writer.writeAlignment(al);
if (test) out << "KEPT SE: " << al.name() << endl;
if (test) out << "KEPT SE: " << al.name() << QT_ENDL;
}
}
else //paired-end reads
Expand All @@ -81,7 +81,7 @@ class ConcreteTool
++c_pe_pass;
writer.writeAlignment(al_cache.take(name));
writer.writeAlignment(al);
if (test) out << "KEPT PE: " << name << endl;
if (test) out << "KEPT PE: " << name << QT_ENDL;
}
else
{
Expand All @@ -92,11 +92,11 @@ class ConcreteTool
}

//write debug output
out << "SE reads : " << c_se << endl;
out << "SE reads (written) : " << c_se_pass << endl;
out << "PE reads : " << c_pe << endl;
out << "PE reads (written) : " << c_pe_pass << endl;
out << "PE reads unmatched (skipped): " << al_cache.size() << endl;
out << "SE reads : " << c_se << QT_ENDL;
out << "SE reads (written) : " << c_se_pass << QT_ENDL;
out << "PE reads : " << c_pe << QT_ENDL;
out << "PE reads (written) : " << c_pe_pass << QT_ENDL;
out << "PE reads unmatched (skipped): " << al_cache.size() << QT_ENDL;
}
};

Expand Down
6 changes: 3 additions & 3 deletions src/BamExtract/main.cpp
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Expand Up @@ -42,7 +42,7 @@ class ConcreteTool
ids << line;
}
file->close();
stdout_stream << "Read IDs: " << ids.count() << endl;
stdout_stream << "Read IDs: " << ids.count() << QT_ENDL;

//open intput/output streams
BamReader reader(getInfile("in"), ref);
Expand Down Expand Up @@ -75,10 +75,10 @@ class ConcreteTool
}
}

stdout_stream << "Reads written to 'out': " << c_match<< endl;
stdout_stream << "Reads written to 'out': " << c_match<< QT_ENDL;
if (out2!="")
{
stdout_stream << "Reads written to 'out2': " << c_other << endl;
stdout_stream << "Reads written to 'out2': " << c_other << QT_ENDL;
}
}
};
Expand Down
4 changes: 2 additions & 2 deletions src/BamFilter/main.cpp
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Expand Up @@ -123,8 +123,8 @@ class ConcreteTool

}

out << "pairs passed: " << count_pass << endl;
out << "pairs dropped: " << count_fail << endl;
out << "pairs passed: " << count_pass << QT_ENDL;
out << "pairs dropped: " << count_fail << QT_ENDL;
}

private:
Expand Down
8 changes: 4 additions & 4 deletions src/BamRemoveVariants/main.cpp
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Expand Up @@ -271,10 +271,10 @@ class ConcreteTool

}

out << "pairs passed: " << count_pass << endl;
out << "pairs dropped: " << count_fail << endl;
out << "reads modified: " << count_modified << endl;
out << "skipped reads: " << count_skipped << endl;
out << "pairs passed: " << count_pass << QT_ENDL;
out << "pairs dropped: " << count_fail << QT_ENDL;
out << "reads modified: " << count_modified << QT_ENDL;
out << "skipped reads: " << count_skipped << QT_ENDL;
}

private:
Expand Down
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