goby-io/pom.xml | 61 4 + 57 - 0 !
1 file changed, 4 insertions(+), 57 deletions(-)

 using debian-packaged protoc compiler

goby-distribution/pom.xml | 23 18 + 5 - 0 !
goby-io/pom.xml | 18 18 + 0 - 0 !
2 files changed, 36 insertions(+), 5 deletions(-)

 adding missing dependencies to the various pom.xml files

goby-distribution/src/main/java/org/campagnelab/goby/compression/BZip2ChunkCodec.java | 8 4 + 4 - 0 !
goby-io/pom.xml | 8 8 + 0 - 0 !
2 files changed, 12 insertions(+), 4 deletions(-)

 using the classes of libjbzip2-java as a replacement for bzip2*

goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java | 4 2 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/alignments/processors/LocalSortProcessor.java | 4 2 + 2 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-)

 changing some imports linked to fastutil classes
 Goby 3.3.1 was written for an old fastutil library.

goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentCollectionHandler.java | 4 2 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java | 4 2 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java | 4 2 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java | 8 4 + 4 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/compression/ProtobuffCollectionHandler.java | 4 2 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.java | 4 2 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.java | 4 2 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.java | 4 2 + 2 - 0 !
8 files changed, 18 insertions(+), 18 deletions(-)

 using generatedmessagev3 from protobuf to replace generatedmessage
 The protobuf package has changed quite a bit since the version goby 3.3.1
 relies on was edited.

goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java | 153 99 + 54 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java | 131 101 + 30 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java | 136 119 + 17 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java | 166 143 + 23 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java | 110 81 + 29 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java | 29 25 + 4 - 0 !
6 files changed, 568 insertions(+), 157 deletions(-)

 using classes of commons-cli instead of unpackaged ones

goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java | 15 8 + 7 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactMode.java | 7 4 + 3 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactOldMode.java | 6 4 + 2 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.java | 9 5 + 4 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java | 9 5 + 4 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java | 9 5 + 4 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/RoundTripAlignment.java | 15 8 + 7 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java | 72 49 + 23 - 0 !
8 files changed, 88 insertions(+), 54 deletions(-)

 using the correct samreader api

goby-distribution/src/main/java/org/campagnelab/goby/modes/SplitTranscriptsMode.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 reading class genetranscriptrelationships from goby archive
 The above-named class is in the archive of Goby and thus does not need to be read elsewhere.

goby-distribution/src/main/java/org/campagnelab/goby/modes/EmpiricalPMode.java | 7 6 + 1 - 0 !
1 file changed, 6 insertions(+), 1 deletion(-)

 catch the ioexception launched by close() method of lineiterator

goby-distribution/pom.xml | 5 5 + 0 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java | 22 17 + 5 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/R/TestFisherExact.java | 21 17 + 4 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java | 22 17 + 5 - 0 !
4 files changed, 56 insertions(+), 14 deletions(-)

 computing p-values by hand as gominer is not packaged in debian

goby-distribution/pom.xml | 17 17 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestConcatAlignmentReader.java | 3 3 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestConcatSortedAlignmentReader.java | 4 4 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestRealignmentProcessor.java | 2 2 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestSkipTo.java | 2 2 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImplTest.java | 6 5 + 1 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/ConcatenateAlignmentModeTest.java | 4 3 + 1 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsIndelGenotypes.java | 2 2 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java | 8 8 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/TestLastToCompact.java | 4 4 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReformatCompactReadsMode.java | 2 2 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/TestSortMode.java | 2 2 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/formats/TestCompareGroupsVCFOutputFormat.java | 3 3 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/predictions/MergeIndelFromTest.java | 5 4 + 1 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java | 3 3 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java | 2 2 + 0 - 0 !
16 files changed, 66 insertions(+), 3 deletions(-)

 modify a few tests when requiring unpackaged tools
 junitx.framework is not packaged, the test files TestSplicedSamHelper.java and
 TestAlignmentReader.java, that use it, are deactivated in
 goby-distribution/pom.xml.
 We also exclude TestGobyPaperTop5000s.java in this pom, as data files that it
 uses are not provided in the source.
 Two tests in TestSamRecordParser are skipped for the same reason.
 One test in TestConcatAlignmentReader needs a file that does not exist.
 The tests in TestIterateSortedAlignment all use a file that does not exist.
 One test in TestSkipTo needs to use the network.
 One test in TestStatistics is skipped as it expects a Fisher test p-value
 greater than 0.05, which seems false after a check with R and also with a
 script using libdistlib-java.
 Tests in TestDiscoverSequenceVariantsIndelGenotypes and in
 TestDiscoverSequenceVariantsMode need genotype.jar or somatic.jar,
 which are not in this package nor in a dependency.
 .
 Also I removed some tests that fail even in a classic Maven build. Maybe this
 is wrong, but anyway they are not run in the classic Maven build and so I am
 unsure upstream has kept them up to date. I opened an issue at the link below.
 Ignored tests are:
 - three tests in TestConcatSortedAlignmentReader;
 - all tests in TestIteratedSortedAlignment2;
 - one test in TestRealignmentProcessor;
 - all tests in TestDiscoverSVMethylationRatesMode;
 - five tests in TestDiscoverSequenceVariantsMode;
 - three tests in TestLastToCompact;
 - one test in TestReformatCompactReadsMode;
 - one test in TestSortMode;
 - two tests in TestCompareGroupsVCFOutputFormat;
 - two tests in MergeIndelFromTest.
 .
 Finally, I removed the tests
 - in ConcatenateAlignmentModeTest.java (one test);
 - HTSJDKReaderImplTest.testReadingBAM;
 - HTSJDKReaderImplTest.testWithPosition;
 - HTSJDKReaderImplTest.testWithSlices;
 - TestConcatAlignmentReader.testConcatSamBam
 which succeed, but need a lot of large data files which I removed when
 repacking.

goby | 52 26 + 26 - 0 !
1 file changed, 26 insertions(+), 26 deletions(-)

 modifying the launcher script to account for debian paths

goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractGobyMode.java | 2 1 + 1 - 0 !
goby-distribution/src/main/java/org/campagnelab/goby/modes/GobyDriver.java | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 ensuring the correct debian path of the goby jar will show up
 This is important for usage messages that are printed when the user invokes
 goby with --help.

goby-distribution/pom.xml | 5 5 + 0 - 0 !
1 file changed, 5 insertions(+)

 adding missing jaxb-api dependency in pom

cpp/configure.ac | 4 2 + 2 - 0 !
cpp/goby.pc.in | 4 2 + 2 - 0 !
cpp/src/GsnapParseTest1.cc | 55 45 + 10 - 0 !
cpp/src/Makefile.am | 6 3 + 3 - 0 !
cpp/src/goby/C_Alignments.cc | 78 69 + 9 - 0 !
cpp/src/goby/C_Gsnap.cc | 55 43 + 12 - 0 !
6 files changed, 164 insertions(+), 38 deletions(-)

 switching from pcre3 to pcre2
 This was tested by running pcreTest (in cpp/src/GsnapParseTest1.cc)
 successfully. Yet I did not compile the other files.

goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java | 1 1 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReadQualityStatsMode.java | 3 3 + 0 - 0 !
goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReformatCompactReadsMode.java | 12 12 + 0 - 0 !
3 files changed, 16 insertions(+)

 omit tests that fail randomly

goby-distribution/pom.xml | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 adding a --add-opens argument needed to run the tests, starting
 from OpenJDK17.