This is an automated email from the git hooks/post-receive script. malex-guest pushed a change to branch upstream in repository subread.
from 32f5127 Imported Upstream version 1.5.0+dfsg new 5acf640 Imported Upstream version 1.5.0-p1+dfsg The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: doc/SubreadUsersGuide.tex | 77 +- src/HelperFunctions.c | 17 +- src/HelperFunctions.h | 4 +- src/Makefile.FreeBSD | 11 +- src/Makefile.Linux | 9 + src/Makefile.MacOS | 10 + src/SNPCalling.c | 10 +- src/SUBindel.c | 2 +- src/SeekGZ.h | 10 - src/build-sam-index.c | 5 +- src/core-indel.c | 27 +- src/core-interface-aligner.c | 45 +- src/core-interface-subjunc.c | 61 +- src/core-junction.c | 68 +- src/core-junction.h | 2 +- src/core.c | 178 +- src/core.h | 5 + src/coverage_calc.c | 32 +- src/fullscan.c | 4 +- src/gene-algorithms.c | 14 +- src/gene-algorithms.h | 4 +- src/gene-value-index.c | 7 +- src/gene-value-index.h | 2 +- src/index-builder.c | 64 +- src/input-files.c | 541 ++- src/input-files.h | 14 +- src/makefile.version | 2 +- src/mergeVCF.c | 2 +- src/read-repair.c | 29 +- src/readSummary.c | 443 +- src/sambam-file.c | 45 +- src/sambam-file.h | 4 +- src/seek-zlib.c | 32 +- src/sorted-hashtable.c | 48 +- src/sorted-hashtable.h | 3 +- src/subread.h | 10 +- src/t.c | 4 - test/featureCounts/data/across_genes.gtf | 8 + test/featureCounts/data/across_genes_r1.bam | Bin 0 -> 231 bytes test/featureCounts/data/across_genes_r1.bam.ora | 8 + test/featureCounts/data/across_genes_r1.sam | 4 + test/featureCounts/data/across_genes_r1.sam.ora | 8 + test/featureCounts/data/across_genes_r2.bam | Bin 0 -> 226 bytes test/featureCounts/data/across_genes_r2.bam.ora | 8 + test/featureCounts/data/across_genes_r2.sam | 4 + test/featureCounts/data/across_genes_r2.sam.ora | 8 + test/featureCounts/data/across_intron.gtf | 3 + test/featureCounts/data/across_intron_r1.bam | Bin 0 -> 245 bytes test/featureCounts/data/across_intron_r1.bam.ora | 3 + test/featureCounts/data/across_intron_r1.sam | 5 + test/featureCounts/data/across_intron_r1.sam.ora | 3 + test/featureCounts/data/across_intron_r2.bam | Bin 0 -> 245 bytes test/featureCounts/data/across_intron_r2.bam.ora | 3 + test/featureCounts/data/across_intron_r2.sam | 5 + test/featureCounts/data/across_intron_r2.sam.ora | 3 + test/featureCounts/data/compare.sh | 15 +- test/featureCounts/data/corner-BothEnds.ora | 8 + test/featureCounts/data/corner-CHIMERIC.ora | 10 - test/featureCounts/data/corner-CHIMERIC.sam | 27 - test/featureCounts/data/corner-Chimeric.ora | 8 + test/featureCounts/data/corner-DoNotSort.ora | 8 + test/featureCounts/data/corner-Extend3.ora | 8 + test/featureCounts/data/corner-Extend5.ora | 8 + test/featureCounts/data/corner-Fraction.ora | 8 + test/featureCounts/data/corner-IgnoreDup.ora | 8 + test/featureCounts/data/corner-Jcounts-FA.ora | 8 + .../data/corner-Jcounts-FA.ora.jcounts | 277 ++ test/featureCounts/data/corner-Jcounts.ora | 8 + test/featureCounts/data/corner-Jcounts.ora.jcounts | 277 ++ test/featureCounts/data/corner-LargestOverlap.ora | 8 + test/featureCounts/data/corner-MaxOPs.ora | 8 + test/featureCounts/data/corner-MinMAPQ.ora | 8 + test/featureCounts/data/corner-MinOverlap.ora | 8 + test/featureCounts/data/corner-MultiMapping.ora | 8 + test/featureCounts/data/corner-PEdist.ora | 8 + test/featureCounts/data/corner-Read2Pos3.ora | 8 + test/featureCounts/data/corner-Read2Pos5.ora | 8 + test/featureCounts/data/intron_between.bam | Bin 0 -> 221 bytes test/featureCounts/data/intron_between.bam.ora | 2 + test/featureCounts/data/intron_between.gtf | 2 + test/featureCounts/data/intron_between.sam | 4 + test/featureCounts/data/intron_between.sam.ora | 2 + .../featureCounts/data/intron_between_nointron.bam | Bin 0 -> 206 bytes .../data/intron_between_nointron.bam.ora | 2 + .../featureCounts/data/intron_between_nointron.sam | 4 + .../data/intron_between_nointron.sam.ora | 2 + .../data/{test-minimum.sam => test-dup.sam} | 600 +-- test/featureCounts/data/test-junc.sam | 5000 ++++++++++++++++++++ test/featureCounts/featureCounts-test.sh | 2 +- test/featureCounts/test_commonusage.sh | 62 + test/featureCounts/test_corner_cases.sh | 24 + test/featureCounts/test_featurelevel.sh | 11 + 92 files changed, 7555 insertions(+), 822 deletions(-) delete mode 100644 src/SeekGZ.h delete mode 100644 src/t.c create mode 100644 test/featureCounts/data/across_genes.gtf create mode 100644 test/featureCounts/data/across_genes_r1.bam create mode 100644 test/featureCounts/data/across_genes_r1.bam.ora create mode 100644 test/featureCounts/data/across_genes_r1.sam create mode 100644 test/featureCounts/data/across_genes_r1.sam.ora create mode 100644 test/featureCounts/data/across_genes_r2.bam create mode 100644 test/featureCounts/data/across_genes_r2.bam.ora create mode 100644 test/featureCounts/data/across_genes_r2.sam create mode 100644 test/featureCounts/data/across_genes_r2.sam.ora create mode 100644 test/featureCounts/data/across_intron.gtf create mode 100644 test/featureCounts/data/across_intron_r1.bam create mode 100644 test/featureCounts/data/across_intron_r1.bam.ora create mode 100644 test/featureCounts/data/across_intron_r1.sam create mode 100644 test/featureCounts/data/across_intron_r1.sam.ora create mode 100644 test/featureCounts/data/across_intron_r2.bam create mode 100644 test/featureCounts/data/across_intron_r2.bam.ora create mode 100644 test/featureCounts/data/across_intron_r2.sam create mode 100644 test/featureCounts/data/across_intron_r2.sam.ora create mode 100644 test/featureCounts/data/corner-BothEnds.ora delete mode 100644 test/featureCounts/data/corner-CHIMERIC.ora delete mode 100644 test/featureCounts/data/corner-CHIMERIC.sam create mode 100644 test/featureCounts/data/corner-Chimeric.ora create mode 100644 test/featureCounts/data/corner-DoNotSort.ora create mode 100644 test/featureCounts/data/corner-Extend3.ora create mode 100644 test/featureCounts/data/corner-Extend5.ora create mode 100644 test/featureCounts/data/corner-Fraction.ora create mode 100644 test/featureCounts/data/corner-IgnoreDup.ora create mode 100644 test/featureCounts/data/corner-Jcounts-FA.ora create mode 100644 test/featureCounts/data/corner-Jcounts-FA.ora.jcounts create mode 100644 test/featureCounts/data/corner-Jcounts.ora create mode 100644 test/featureCounts/data/corner-Jcounts.ora.jcounts create mode 100644 test/featureCounts/data/corner-LargestOverlap.ora create mode 100644 test/featureCounts/data/corner-MaxOPs.ora create mode 100644 test/featureCounts/data/corner-MinMAPQ.ora create mode 100644 test/featureCounts/data/corner-MinOverlap.ora create mode 100644 test/featureCounts/data/corner-MultiMapping.ora create mode 100644 test/featureCounts/data/corner-PEdist.ora create mode 100644 test/featureCounts/data/corner-Read2Pos3.ora create mode 100644 test/featureCounts/data/corner-Read2Pos5.ora create mode 100644 test/featureCounts/data/intron_between.bam create mode 100644 test/featureCounts/data/intron_between.bam.ora create mode 100644 test/featureCounts/data/intron_between.gtf create mode 100644 test/featureCounts/data/intron_between.sam create mode 100644 test/featureCounts/data/intron_between.sam.ora create mode 100644 test/featureCounts/data/intron_between_nointron.bam create mode 100644 test/featureCounts/data/intron_between_nointron.bam.ora create mode 100644 test/featureCounts/data/intron_between_nointron.sam create mode 100644 test/featureCounts/data/intron_between_nointron.sam.ora copy test/featureCounts/data/{test-minimum.sam => test-dup.sam} (77%) create mode 100644 test/featureCounts/data/test-junc.sam create mode 100644 test/featureCounts/test_commonusage.sh create mode 100644 test/featureCounts/test_featurelevel.sh -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit