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../
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data
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4114
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Peter |
new class for one-way ANOVA test
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yat-hello
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updating copyright years
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alignment2.cc
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alignment.cc
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anova.cc
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new class for one-way ANOVA test
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averager1.cc
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averager3.cc
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2881
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averager4.cc
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2881
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averager.cc
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4359
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bam.cc
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12.3 KB
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bam_header2.cc
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1.7 KB
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3999
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bam_header.cc
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bam_iterator.cc
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3.7 KB
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3999
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bam_multi_region_iterator.cc
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2.8 KB
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4272
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8 months
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Peter |
closes #774. Create multi-region iterator.
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bam_pair.cc
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1.7 KB
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3883
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Peter |
remove support for building against libbam (which allows us to remove …
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bam_pair_analyse.cc
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1.7 KB
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3999
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bam_pair_buffer.cc
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2.7 KB
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4057
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2 years
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Peter |
closes #798; new classes BamPairBuffer? and a more general SortedBuffer?.
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bam_pair_iterator2.cc
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2.2 KB
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3883
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Peter |
remove support for building against libbam (which allows us to remove …
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bam_pair_iterator.cc
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2.5 KB
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3999
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bam_read_filter.cc
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1.7 KB
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3999
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bam_read_sequence_iterator.cc
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2.3 KB
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4345
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Peter |
new class BamReadSequenceIterator?
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bam_region_iterator.cc
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2.6 KB
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3999
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3 years
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Peter |
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binary_read_write.cc
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2.6 KB
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3910
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3 years
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Peter |
add missing file
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chi2.cc
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1.9 KB
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3726
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6 years
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Peter |
correct include
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cholesky_decomposer.cc
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2.8 KB
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4341
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increase error margin to avoid spurious test failure. (reported by jari)
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cigar2.cc
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1.7 KB
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3342
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9 years
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Peter |
merge 0.12.2 into trunk
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cigar.cc
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4.3 KB
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4207
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13 months
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Peter |
update copyright statements
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cigar_iterator.cc
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2.8 KB
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3417
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Peter |
updating copyright statements
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cmd_test.sh
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981 bytes
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4207
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codon.cc
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1.8 KB
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4359
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commandline.cc
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18.2 KB
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4359
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concept.cc
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2.3 KB
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4200
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removing trailing whitespace and empty lines at bottom of files.
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consensus_inputranker.cc
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3.2 KB
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4359
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Peter |
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copy_k_of_n.cc
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1.7 KB
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3454
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8 years
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Peter |
closes #838
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cox.cc
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4.8 KB
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4252
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10 months
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Peter |
merge 0.20 release into trunk
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crossvalidation.cc
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2.5 KB
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4359
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Peter |
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data_lookup_1d.cc
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5.7 KB
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4359
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data_weight.cc
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1.6 KB
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4359
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data_weight_proxy.cc
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3.1 KB
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4359
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defs.sh.in
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4.9 KB
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4359
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deleter.cc
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1.2 KB
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4089
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Peter |
updating copyright years
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diagonal_matrix.cc
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3.8 KB
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4359
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distance.cc
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9.0 KB
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3550
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Peter |
Update copyright years. Happy New Year
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dna.cc
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3.4 KB
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2881
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11 years
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Peter |
Define PP variables in config.h rather than in CPPFLAGS. Include …
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dna_reverse_complement.cc
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2.3 KB
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3628
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Peter |
merge release 0.14.2 into trunk
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doxygen_test.sh
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1.7 KB
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4062
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merged r4061 into trunk
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ensemble.cc
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5.7 KB
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4359
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fasta.cc
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2.6 KB
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3999
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Peter |
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feature_selection.cc
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3.4 KB
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4359
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5 weeks
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Peter |
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fileutil.cc
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6.6 KB
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4359
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Peter |
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fisher.cc
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6.4 KB
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3743
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Peter |
merge release 0.15.1 into trunk
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gaussian_mixture.cc
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2.9 KB
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4200
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Peter |
removing trailing whitespace and empty lines at bottom of files.
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gen_libmy_shared.sh
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1.8 KB
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3999
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Peter |
update copyright years
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gen_libmy_static.sh
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1.5 KB
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3130
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merge release 0.11 into trunk
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genomic_position.cc
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1.4 KB
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4359
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Peter |
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getline_iterator.cc
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2.0 KB
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4359
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Peter |
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getvector.cc
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2.5 KB
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3930
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Peter |
merge release 0.17.1 into trunk
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gff.cc
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4.7 KB
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3875
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4 years
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Peter |
merge release 0.17 into trunk
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gsl_error_handler.cc
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1.4 KB
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3963
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3 years
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Peter |
new function supposed to be used by GSL error handler, resulting in a …
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help_test.sh
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1.3 KB
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4207
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13 months
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Peter |
update copyright statements
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histogram.cc
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2.2 KB
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4359
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5 weeks
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Peter |
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igp.cc
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1.4 KB
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4359
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Peter |
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index.cc
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2.7 KB
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4359
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Peter |
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init.sh
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2.9 KB
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4312
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when tests create write-protected files the removal in 'init.sh' would …
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inputranker.cc
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1.9 KB
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4359
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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interpolation.cc
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3.8 KB
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3966
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3 years
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Peter |
merge changes in 0.17-stable branch (since 0.17.1) into trunk.
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inverse_svd.cc
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3.0 KB
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4285
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8 months
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Peter |
simplify code with test code recently added to.
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is_sorted_until.cc
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3.3 KB
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4349
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2 months
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Peter |
adding function is_sorted_until for input iterators.
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iterator.cc
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23.2 KB
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4359
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5 weeks
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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kalman_filter.cc
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2.2 KB
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4287
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8 months
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Peter |
add class for KalmanFilter?
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kaplan_meier.cc
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3.1 KB
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4255
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9 months
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Peter |
add class doing Kaplan-Meier estimations
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kendall.cc
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5.6 KB
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4110
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Peter |
merge release 0.19 into trunk
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kernel.cc
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7.2 KB
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4359
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Peter |
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kernel_lookup.cc
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5.4 KB
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4359
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Peter |
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kernel_matrix.cc
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1.6 KB
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3190
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9 years
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Peter |
new class KernelMatrix?. closes #381
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kernel_pca.cc
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4.3 KB
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4359
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5 weeks
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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knn.cc
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11.2 KB
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4359
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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kolmogorov_smirnov.cc
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7.3 KB
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3018
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10 years
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Peter |
merge patch release 0.10.2 into trunk
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large_file.cc
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1.6 KB
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4359
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5 weeks
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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libbam.cc
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1.4 KB
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3888
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4 years
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Peter |
fix compilation errors in --with-htslib mode introduced in r3883, refs #939
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likelihood.cc
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2.7 KB
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4289
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8 months
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Peter |
add a class Likelihood; closes #988
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likelihood_ratio_test_binomial.cc
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1.4 KB
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3138
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10 years
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Peter |
change name of class and implement function llr(). closes #769
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ln_pdf.cc
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6.0 KB
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4336
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5 months
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Peter |
a set of new functions calculating logarithm of pdf for various …
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Makefile
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798 bytes
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2749
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11 years
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Peter |
add small convenience Makefiles in subdirs. closes #703
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Makefile.am
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14.6 KB
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4363
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2 weeks
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Peter |
skeleton to support case rows < columns and add more tests for PCA …
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mAligner.cc
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4.8 KB
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4353
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5 weeks
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Peter |
refactor the mAligner class to allow more flexible usage for inherited …
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matrix.cc
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10.1 KB
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4207
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13 months
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Peter |
update copyright statements
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matrix_expression.cc
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4.6 KB
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4207
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13 months
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Peter |
update copyright statements
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matrix_lookup.cc
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6.3 KB
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4359
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Peter |
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matrix_lookup_weighted.cc
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3.3 KB
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4359
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Peter |
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matrix_view.cc
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7.5 KB
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4207
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13 months
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Peter |
update copyright statements
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matrix_weighted.cc
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3.1 KB
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4359
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Peter |
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merge.cc
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3.3 KB
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4359
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Peter |
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merge_iterator.cc
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3.7 KB
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3417
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8 years
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Peter |
updating copyright statements
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minimizer.cc
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1.9 KB
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4252
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10 months
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Peter |
merge 0.20 release into trunk
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msmith_waterman2.cc
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4.1 KB
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4353
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5 weeks
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Peter |
refactor the mAligner class to allow more flexible usage for inherited …
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multiminimizer.cc
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2.0 KB
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4252
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10 months
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Peter |
merge 0.20 release into trunk
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multiminimizerderivative.cc
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2.3 KB
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4252
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10 months
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Peter |
merge 0.20 release into trunk
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multiprocess.cc
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2.2 KB
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4252
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10 months
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Peter |
merge 0.20 release into trunk
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multivariate.cc
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2.3 KB
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4130
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20 months
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Peter |
Add function fit2 taking new class MatrixBase?. Keep the old interface …
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multivariate_gaussian.cc
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2.5 KB
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4281
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8 months
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Peter |
Random generator from a Multivariate Gaussian Distribution. closes #983
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nbc.cc
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1.8 KB
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4359
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5 weeks
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Peter |
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ncc.cc
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11.4 KB
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4359
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Peter |
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needleman_wunsch2.cc
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1.6 KB
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4334
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6 months
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Peter |
new class NeedlemanWunsch?.
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needleman_wunsch.cc
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2.0 KB
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4308
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8 months
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Peter |
merge release 0.20.1 into trunk.
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negative_binomial.cc
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5.1 KB
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3999
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3 years
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Peter |
update copyright years
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negative_binomial_extended_mixture.cc
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3.0 KB
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4192
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14 months
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Peter |
New class NegativeBinomialExtendedMixture?, a variant of Negative …
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negative_binomial_mixture.cc
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3.0 KB
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4184
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15 months
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Peter |
class to model mixture model of NegativeBinomials?, refs #979
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nni.cc
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5.9 KB
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4359
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normalization.cc
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24.4 KB
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4252
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merge 0.20 release into trunk
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ostream_iterator.cc
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1.6 KB
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3152
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Peter |
add missing source file. refs #770
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pca2.cc
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8.3 KB
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4370
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provide projection function taking (and returning) vector. refs #216.
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pca.cc
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1.6 KB
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2919
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Peter |
update copyright years
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percentile_confidence_interval.cc
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2.9 KB
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4036
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3 years
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Peter |
closes #963. New class PercentileConfidenceInterval?
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perceptron.cc
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5.3 KB
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3709
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6 years
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Peter |
new class that impements a Perceptron - special case of multivariate …
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phred.cc
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1.4 KB
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3325
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9 years
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Peter |
new functions phred and phred_inv that calculate phred scaled …
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pileup.cc
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8.8 KB
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3999
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3 years
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Peter |
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poisson.cc
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4.1 KB
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3662
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Peter |
close #882
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poisson_mixture.cc
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2.4 KB
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4184
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class to model mixture model of NegativeBinomials?, refs #979
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print_what.cc
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1.7 KB
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3938
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Peter |
let configure fail if compiler is not a C++11 compiler. …
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priority_queue.cc
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2.4 KB
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3999
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3 years
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Peter |
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queue2.cc
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1.9 KB
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3999
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3 years
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queue3.cc
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2.6 KB
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4043
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Peter |
Add capacity to Queue and PriorityQueue?, which is a feature to limit …
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queue.cc
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1.7 KB
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3999
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3 years
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update copyright years
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random_shuffle.cc
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1.4 KB
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4252
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merge 0.20 release into trunk
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random_shuffle.sh
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1.0 KB
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4252
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merge 0.20 release into trunk
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range.cc
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1.5 KB
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3330
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Peter |
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ranking.cc
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8.5 KB
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4083
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merge kendall-score branch into trunk. refs #710
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README
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4.6 KB
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4359
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regression.cc
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17.2 KB
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4359
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rnd.cc
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2.4 KB
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4207
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update copyright statements
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rng-mt.cc
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3.6 KB
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3999
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update copyright years
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roc.cc
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11.8 KB
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4359
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root_finder.cc
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2.2 KB
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4252
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merge 0.20 release into trunk
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root_finder_derivative.cc
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2.0 KB
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4252
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Peter |
merge 0.20 release into trunk
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round.cc
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1.8 KB
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4059
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2 years
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Peter |
new function: round, which is rounding elements in a range with the …
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scheduler2.cc
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2.6 KB
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3855
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4 years
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Peter |
updating copyright statements
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scheduler3.cc
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2.3 KB
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4204
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Peter |
merge release 0.19.2 into trunk
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scheduler4.cc
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1.9 KB
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3686
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6 years
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Peter |
only send jobs to queue if they have been submitted
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scheduler5.cc
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1.9 KB
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3823
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4 years
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Peter |
Merge release 0.16 into trunk
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scheduler6.cc
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2.0 KB
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3828
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Peter |
Make the Scheduler recyclable i.e. allow jobs to be submitted also …
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scheduler7.cc
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2.3 KB
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3848
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Peter |
add functionality to alter number of threads used by Scheduler. closes #910
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scheduler8.cc
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2.5 KB
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4164
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19 months
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Peter |
Merge release 0.19.1 into trunk
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scheduler9.cc
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2.2 KB
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4164
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19 months
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Peter |
Merge release 0.19.1 into trunk
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scheduler.cc
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2.5 KB
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3851
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4 years
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Peter |
merge release 0.16.3 into trunk.
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score.cc
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3.9 KB
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4359
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5 weeks
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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segment.cc
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14.6 KB
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4252
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10 months
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Peter |
merge 0.20 release into trunk
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shuffle.cc
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1.2 KB
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4359
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5 weeks
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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smart_ptr.cc
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1.3 KB
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4359
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Peter |
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smith_waterman.cc
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1.8 KB
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3209
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9 years
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Peter |
add missing source file and fix compilation error --without-samtools
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smoother.cc
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1.8 KB
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3550
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7 years
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Peter |
Update copyright years. Happy New Year
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spearman.cc
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4.7 KB
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2919
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11 years
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Peter |
update copyright years
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split.cc
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2.9 KB
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4207
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13 months
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Peter |
update copyright statements
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statistics.cc
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13.4 KB
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4359
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Peter |
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stdopt.cc
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Peter |
update copyright statements
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stream_redirect.cc
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3.7 KB
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Peter |
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subset_generator.cc
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11.2 KB
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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Suite.cc
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5.1 KB
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Peter |
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Suite.h
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22.4 KB
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Peter |
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svd.cc
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5.0 KB
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4367
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13 days
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Peter |
improve docs and test of SVD class.
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svm.cc
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4.6 KB
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4359
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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svm_multi_class.cc
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4.9 KB
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4359
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Peter |
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target.cc
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3.5 KB
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Peter |
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ttest.cc
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1.7 KB
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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tukey.cc
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2.7 KB
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3875
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4 years
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Peter |
merge release 0.17 into trunk
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unity_scaler.cc
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947 bytes
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4164
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19 months
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Peter |
Merge release 0.19.1 into trunk
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utility.cc
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24.4 KB
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4359
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5 weeks
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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vcf.cc
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8.0 KB
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4316
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7 months
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Peter |
Merged release 0.20.2 into trunk
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vcf_compare.cc
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1004 bytes
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3759
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5 years
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Peter |
refs #905. New class, VcfCompare?, to compare to VCF objects used e.g. …
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vcf_file2.cc
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1.1 KB
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4252
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10 months
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Peter |
merge 0.20 release into trunk
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vcf_file3.cc
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1.1 KB
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4045
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3 years
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Peter |
add missing file
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vcf_file.cc
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2.1 KB
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3774
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5 years
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Peter |
implement VcfIterator?. refs #905
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vcf_header.cc
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3.1 KB
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4308
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8 months
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Peter |
merge release 0.20.1 into trunk.
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vector.cc
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13.9 KB
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4359
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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vector_expression.cc
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6.1 KB
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3677
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6 years
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Peter |
refs #897; some tests for bug #897
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version.cc
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2.1 KB
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4359
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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version_option_test.sh
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1.3 KB
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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view.cc
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6.1 KB
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4359
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Peter |
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weighted_iterator_archetype.cc
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5.4 KB
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3579
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7 years
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Peter |
merge release 0.14 into trunk
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yat_ac_write_to_file_test.sh
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4.0 KB
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4326
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7 months
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Peter |
We had two macros with very similar behaviour: YAT_AC_APPEND in …
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yat_am_local_test.sh
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1.7 KB
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4326
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7 months
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Peter |
We had two macros with very similar behaviour: YAT_AC_APPEND in …
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yat_config_cblas_test.sh
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1.0 KB
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3114
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10 years
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Peter |
update copyright years
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yat_config_test.sh
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1.7 KB
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3855
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4 years
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Peter |
updating copyright statements
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yat_cpp_add_flag_test.sh
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1.6 KB
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3114
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Peter |
update copyright years
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yat_cxx_add_flag_test.sh
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1.5 KB
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3114
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Peter |
update copyright years
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yat_have_svn_wc_test.sh
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1.1 KB
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3999
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3 years
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Peter |
update copyright years
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yat_header_assert_test.sh
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1.2 KB
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3855
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Peter |
updating copyright statements
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yat_ld_add_flag_test.sh
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1.6 KB
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3114
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Peter |
update copyright years
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yat_lt_compile_ifelse_test.sh
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2.0 KB
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3855
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Peter |
updating copyright statements
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yat_lt_link_ifelse_test.sh
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3855
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Peter |
updating copyright statements
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yat_lt_link_la_ifelse_test.sh
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1.5 KB
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3855
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Peter |
updating copyright statements
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yat_m4_test2.sh
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1.5 KB
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3999
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3 years
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Peter |
update copyright years
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yat_m4_test.sh
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1.7 KB
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3855
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Peter |
updating copyright statements
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yat_m4_with_bam_test.sh
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1.4 KB
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3855
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Peter |
updating copyright statements
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yat_msg_error_test2.sh
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3330
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Peter |
update copyright years
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yat_msg_error_test.sh
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1.5 KB
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3855
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4 years
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Peter |
updating copyright statements
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yat_pc_test.sh
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3.2 KB
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4019
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3 years
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Peter |
merge 0.18 into trunk
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yat_prog_move_if_change_test.sh
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1.3 KB
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4359
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5 weeks
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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yat_revision_header_test.sh
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1.6 KB
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3855
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Peter |
updating copyright statements
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yat_svn_release_year_test.sh
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1.9 KB
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4359
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Peter |
update copyright years using svndigest 0.11 (in contrast to 0.10.x …
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yat_svn_revision_test.sh
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3999
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Peter |
update copyright years
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yat_svn_timestamp_test.sh
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1.6 KB
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4323
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7 months
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Peter |
the rules for timestamp require the revision files to be present, so …
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yat_use_libtool_tag_test.sh
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1.4 KB
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3330
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Peter |
update copyright years
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