[med-svn] [ea-utils] 04/04: Merge tag 'upstream/1.04.807+dfsg'
Andreas Tille
tille at debian.org
Mon May 8 17:17:48 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ea-utils.
commit 599e90089e8e1c7974751380bdb053531f50afab
Merge: 90501c6 0bd5483
Author: Andreas Tille <tille at debian.org>
Date: Mon May 8 19:16:58 2017 +0200
Merge tag 'upstream/1.04.807+dfsg'
Upstream version 1.04.807+dfsg
README.md | 5 +
bam.c | 474 -
bam_aux.c | 213 -
bam_cat.c | 185 -
bam_import.c | 489 -
bam_index.c | 724 -
bam_lpileup.c | 198 -
bam_md.c | 389 -
bam_pileup.c | 437 -
bam_reheader.c | 62 -
bam_sort.c | 566 -
bedidx.c | 162 -
bgzf.c | 694 -
CHANGES => clipper/CHANGES | 13 +
clipper/Chrdex.pm | 479 +
clipper/Grun.pm | 114 +
clipper/HyperLevelDB/.gitignore | 34 +
clipper/HyperLevelDB/.tarballignore | 2 +
clipper/HyperLevelDB/AUTHORS | 15 +
clipper/HyperLevelDB/LICENSE | 27 +
clipper/HyperLevelDB/Makefile.am | 274 +
clipper/HyperLevelDB/NEWS | 17 +
clipper/HyperLevelDB/README | 62 +
clipper/HyperLevelDB/TODO | 14 +
clipper/HyperLevelDB/benchmark.cc | 187 +
clipper/HyperLevelDB/configure.ac | 111 +
clipper/HyperLevelDB/db/autocompact_test.cc | 123 +
clipper/HyperLevelDB/db/builder.cc | 88 +
clipper/HyperLevelDB/db/builder.h | 34 +
clipper/HyperLevelDB/db/c.cc | 595 +
clipper/HyperLevelDB/db/c_test.c | 390 +
clipper/HyperLevelDB/db/corruption_test.cc | 374 +
clipper/HyperLevelDB/db/db_bench.cc | 979 +
clipper/HyperLevelDB/db/db_impl.cc | 1991 ++
clipper/HyperLevelDB/db/db_impl.h | 269 +
clipper/HyperLevelDB/db/db_iter.cc | 320 +
clipper/HyperLevelDB/db/db_iter.h | 28 +
clipper/HyperLevelDB/db/db_test.cc | 2228 ++
clipper/HyperLevelDB/db/dbformat.cc | 140 +
clipper/HyperLevelDB/db/dbformat.h | 232 +
clipper/HyperLevelDB/db/dbformat_test.cc | 112 +
clipper/HyperLevelDB/db/filename.cc | 144 +
clipper/HyperLevelDB/db/filename.h | 85 +
clipper/HyperLevelDB/db/filename_test.cc | 123 +
clipper/HyperLevelDB/db/leveldb_main.cc | 238 +
clipper/HyperLevelDB/db/log_format.h | 35 +
clipper/HyperLevelDB/db/log_reader.cc | 266 +
clipper/HyperLevelDB/db/log_reader.h | 108 +
clipper/HyperLevelDB/db/log_test.cc | 539 +
clipper/HyperLevelDB/db/log_writer.cc | 132 +
clipper/HyperLevelDB/db/log_writer.h | 50 +
clipper/HyperLevelDB/db/memtable.cc | 180 +
clipper/HyperLevelDB/db/memtable.h | 95 +
clipper/HyperLevelDB/db/repair.cc | 461 +
clipper/HyperLevelDB/db/replay_iterator.cc | 220 +
clipper/HyperLevelDB/db/replay_iterator.h | 73 +
clipper/HyperLevelDB/db/skiplist.h | 460 +
clipper/HyperLevelDB/db/skiplist_test.cc | 378 +
clipper/HyperLevelDB/db/snapshot.h | 66 +
clipper/HyperLevelDB/db/table_cache.cc | 127 +
clipper/HyperLevelDB/db/table_cache.h | 61 +
clipper/HyperLevelDB/db/version_edit.cc | 266 +
clipper/HyperLevelDB/db/version_edit.h | 107 +
clipper/HyperLevelDB/db/version_edit_test.cc | 46 +
clipper/HyperLevelDB/db/version_set.cc | 1584 +
clipper/HyperLevelDB/db/version_set.h | 412 +
clipper/HyperLevelDB/db/version_set_test.cc | 179 +
clipper/HyperLevelDB/db/write_batch.cc | 147 +
clipper/HyperLevelDB/db/write_batch_internal.h | 49 +
clipper/HyperLevelDB/db/write_batch_test.cc | 120 +
clipper/HyperLevelDB/doc/bench/db_bench_sqlite3.cc | 718 +
clipper/HyperLevelDB/doc/bench/db_bench_tree_db.cc | 528 +
clipper/HyperLevelDB/doc/benchmark.html | 459 +
clipper/HyperLevelDB/doc/doc.css | 89 +
clipper/HyperLevelDB/doc/impl.html | 213 +
clipper/HyperLevelDB/doc/index.html | 549 +
clipper/HyperLevelDB/doc/log_format.txt | 75 +
clipper/HyperLevelDB/doc/table_format.txt | 104 +
clipper/HyperLevelDB/helpers/memenv/memenv.cc | 383 +
clipper/HyperLevelDB/helpers/memenv/memenv.h | 20 +
clipper/HyperLevelDB/helpers/memenv/memenv_test.cc | 232 +
clipper/HyperLevelDB/hyperleveldb.upack.in | 41 +
clipper/HyperLevelDB/include/hyperleveldb/c.h | 290 +
clipper/HyperLevelDB/include/hyperleveldb/cache.h | 99 +
.../HyperLevelDB/include/hyperleveldb/comparator.h | 67 +
clipper/HyperLevelDB/include/hyperleveldb/db.h | 192 +
clipper/HyperLevelDB/include/hyperleveldb/env.h | 352 +
.../include/hyperleveldb/filter_policy.h | 70 +
.../HyperLevelDB/include/hyperleveldb/iterator.h | 100 +
.../HyperLevelDB/include/hyperleveldb/options.h | 206 +
.../include/hyperleveldb/replay_iterator.h | 65 +
clipper/HyperLevelDB/include/hyperleveldb/slice.h | 109 +
clipper/HyperLevelDB/include/hyperleveldb/status.h | 107 +
clipper/HyperLevelDB/include/hyperleveldb/table.h | 85 +
.../include/hyperleveldb/table_builder.h | 92 +
.../include/hyperleveldb/write_batch.h | 64 +
clipper/HyperLevelDB/issues/issue178_test.cc | 92 +
clipper/HyperLevelDB/issues/issue200_test.cc | 59 +
clipper/HyperLevelDB/leveldb-verify.cc | 205 +
clipper/HyperLevelDB/libhyperleveldb.pc.in | 12 +
clipper/HyperLevelDB/m4/ax_check_compile_flag.m4 | 72 +
clipper/HyperLevelDB/port/README | 10 +
clipper/HyperLevelDB/port/atomic_pointer.h | 224 +
clipper/HyperLevelDB/port/port.h | 19 +
clipper/HyperLevelDB/port/port_example.h | 135 +
clipper/HyperLevelDB/port/port_posix.cc | 54 +
clipper/HyperLevelDB/port/port_posix.h | 171 +
clipper/HyperLevelDB/port/thread_annotations.h | 59 +
clipper/HyperLevelDB/port/win/stdint.h | 24 +
clipper/HyperLevelDB/table/block.cc | 268 +
clipper/HyperLevelDB/table/block.h | 44 +
clipper/HyperLevelDB/table/block_builder.cc | 109 +
clipper/HyperLevelDB/table/block_builder.h | 57 +
clipper/HyperLevelDB/table/filter_block.cc | 111 +
clipper/HyperLevelDB/table/filter_block.h | 68 +
clipper/HyperLevelDB/table/filter_block_test.cc | 128 +
clipper/HyperLevelDB/table/format.cc | 145 +
clipper/HyperLevelDB/table/format.h | 108 +
clipper/HyperLevelDB/table/iterator.cc | 67 +
clipper/HyperLevelDB/table/iterator_wrapper.h | 63 +
clipper/HyperLevelDB/table/merger.cc | 197 +
clipper/HyperLevelDB/table/merger.h | 26 +
clipper/HyperLevelDB/table/table.cc | 275 +
clipper/HyperLevelDB/table/table_builder.cc | 269 +
clipper/HyperLevelDB/table/table_test.cc | 876 +
clipper/HyperLevelDB/table/two_level_iterator.cc | 182 +
clipper/HyperLevelDB/table/two_level_iterator.h | 34 +
clipper/HyperLevelDB/util/arena.cc | 68 +
clipper/HyperLevelDB/util/arena.h | 68 +
clipper/HyperLevelDB/util/arena_test.cc | 68 +
clipper/HyperLevelDB/util/bloom.cc | 95 +
clipper/HyperLevelDB/util/bloom_test.cc | 161 +
clipper/HyperLevelDB/util/cache.cc | 325 +
clipper/HyperLevelDB/util/cache_test.cc | 186 +
clipper/HyperLevelDB/util/coding.cc | 194 +
clipper/HyperLevelDB/util/coding.h | 104 +
clipper/HyperLevelDB/util/coding_test.cc | 196 +
clipper/HyperLevelDB/util/comparator.cc | 102 +
clipper/HyperLevelDB/util/crc32c.cc | 332 +
clipper/HyperLevelDB/util/crc32c.h | 45 +
clipper/HyperLevelDB/util/crc32c_test.cc | 72 +
clipper/HyperLevelDB/util/env.cc | 96 +
clipper/HyperLevelDB/util/env_posix.cc | 778 +
clipper/HyperLevelDB/util/env_test.cc | 104 +
clipper/HyperLevelDB/util/filter_policy.cc | 11 +
clipper/HyperLevelDB/util/hash.cc | 52 +
clipper/HyperLevelDB/util/hash.h | 19 +
clipper/HyperLevelDB/util/histogram.cc | 139 +
clipper/HyperLevelDB/util/histogram.h | 42 +
clipper/HyperLevelDB/util/logging.cc | 81 +
clipper/HyperLevelDB/util/logging.h | 47 +
clipper/HyperLevelDB/util/mutexlock.h | 41 +
clipper/HyperLevelDB/util/options.cc | 30 +
clipper/HyperLevelDB/util/posix_logger.h | 98 +
clipper/HyperLevelDB/util/random.h | 64 +
clipper/HyperLevelDB/util/status.cc | 75 +
clipper/HyperLevelDB/util/testharness.cc | 77 +
clipper/HyperLevelDB/util/testharness.h | 138 +
clipper/HyperLevelDB/util/testutil.cc | 51 +
clipper/HyperLevelDB/util/testutil.h | 53 +
Makefile => clipper/Makefile | 52 +-
README => clipper/README | 4 +
clipper/affy-csv-to-bed.pl | 34 +
clipper/affy-liftover.pl | 97 +
clipper/aggregate-results-by-gene.pl | 294 +
alc => clipper/alc | 0
clipper/align-sw.cpp | 23 +
clipper/bam-filter.cpp | 245 +
clipper/bowtie-gzip.patch | 34 +
clipper/bwa-to-bowtie | 407 +
clipper/check-clipper.sh | 30 +
clipper/contig-stats | 136 +
clipper/count-ambig.cpp | 136 +
clipper/debug | 5 +
determine-phred => clipper/determine-phred | 0
clipper/ea-bcl2fastq.cpp | 646 +
ea-utils.spec => clipper/ea-utils.spec | 2 +-
ea-utils.spec => clipper/ea-utils.spex | 2 +-
clipper/fasta-qual-to-fastq | 54 +
fastq-clipper.c => clipper/fastq-clipper.cpp | 0
fastq-join.c => clipper/fastq-join.cpp | 33 +-
clipper/fastq-join.t | 10 +
fastq-lib.cpp => clipper/fastq-lib.cpp | 167 +-
fastq-lib.h => clipper/fastq-lib.h | 1 +
fastq-mcf.c => clipper/fastq-mcf.cpp | 91 +-
fastq-multx.c => clipper/fastq-multx.cpp | 231 +-
fastq-stats.cpp => clipper/fastq-stats.cpp | 4 +-
clipper/fastq-to-fasta | 36 +
fastx-graph => clipper/fastx-graph | 0
gcModel.c => clipper/gcModel.cpp | 2 +-
gcModel.h => clipper/gcModel.h | 2 +-
clipper/getgenbankannot | 67 +
clipper/getline.c | 103 +
clipper/gff2gtf | 103 +
clipper/grun | 3930 +++
gtf2bed => clipper/gtf2bed | 22 +-
clipper/install-bamtools.sh | 11 +
clipper/master-barcodes.txt | 862 +
clipper/merge-fifo | 54 +
clipper/mirna-quant.cpp | 710 +
clipper/mixfastqs.pl | 18 +
clipper/multx.sh | 3 +
clipper/pbi-clean.cpp | 279 +
clipper/qsh | 455 +
clipper/qsub | 182 +
randomFQ => clipper/randomFQ | 0
sam-stats.cpp => clipper/sam-stats.cpp | 49 +-
clipper/sam-stats.pl | 343 +
clipper/seqsig.cpp | 587 +
clipper/t/in/join/phred.1.fq | 4 +
clipper/t/in/join/phred.2.fq | 4 +
clipper/t/in/join/test-m1.fq | 12 +
clipper/t/in/join/test-m2.fq | 12 +
clipper/t/in/join/test-ov-a.1.fq | 400 +
clipper/t/in/join/test-ov-a.2.fq | 400 +
clipper/t/in/join/test-ov-b.1.fq | 400 +
clipper/t/in/join/test-ov-b.2.fq | 400 +
clipper/t/in/mcf/adap.fa | 2 +
clipper/t/in/mcf/count.fq | 4 +
clipper/t/in/mcf/test-mcf-dup.fq | 24 +
clipper/t/in/mcf/test.fa | 2 +
clipper/t/in/mcf/test1.fq | 32 +
clipper/t/in/mcf/test2.fq | 200 +
clipper/t/in/mcf/test3.fq | 28 +
clipper/t/in/mcf/test4.fq1 | 5 +
clipper/t/in/mcf/test4.fq2 | 5 +
clipper/t/in/mcf/test5.fq | 16 +
clipper/t/in/multx/master-barcodes.txt | 862 +
clipper/t/in/multx/mxtest-h_1.fastq | 1000 +
clipper/t/in/multx/mxtest-h_2.fastq | 1000 +
clipper/t/in/multx/mxtest_1.fastq | 1000 +
clipper/t/in/multx/mxtest_2.fastq | 1000 +
clipper/t/in/multx/mxtest_3.fastq | 1000 +
clipper/t/join.t | 33 +
clipper/t/mcf.t | 36 +
clipper/t/multx.t | 31 +
clipper/t/out/join/test-m.join | 12 +
clipper/t/out/join/test-m.out | 5 +
clipper/t/out/join/test-nov-a.join | 36 +
clipper/t/out/join/test-nov-a.out | 5 +
clipper/t/out/join/test-nov-b.join | 36 +
clipper/t/out/join/test-nov-b.out | 5 +
clipper/t/out/join/test-ov-a.join | 372 +
clipper/t/out/join/test-ov-a.out | 5 +
clipper/t/out/join/test-ov-b.join | 372 +
clipper/t/out/join/test-ov-b.out | 5 +
clipper/t/out/join/test-phred.join | 4 +
clipper/t/out/join/test-phred.out | 5 +
clipper/t/out/mcf/test1.err | 10 +
clipper/t/out/mcf/test1.out | 32 +
clipper/t/out/mcf/test2.err | 62 +
clipper/t/out/mcf/test2.out | 0
clipper/t/out/mcf/test3.err | 10 +
clipper/t/out/mcf/test3.out | 32 +
clipper/t/out/mcf/test4.err | 9 +
clipper/t/out/mcf/test4.out1 | 4 +
clipper/t/out/mcf/test4.out2 | 4 +
clipper/t/out/mcf/test5.err | 11 +
clipper/t/out/mcf/test5.out | 28 +
clipper/t/out/mcf/test6.err | 10 +
clipper/t/out/mcf/test6.out.gz | Bin 0 -> 324 bytes
clipper/t/out/mcf/test7.err | 9 +
clipper/t/out/mcf/test7.out | 16 +
clipper/t/out/mcf/test8.err | 0
clipper/t/out/mcf/test8.out | 8 +
clipper/t/out/mcf/test9.err | 9 +
clipper/t/out/mcf/test9.out | 16 +
clipper/t/out/multx/test1.err | 5 +
clipper/t/out/multx/test1.out | 7 +
clipper/t/out/multx/test2.err | 5 +
clipper/t/out/multx/test2.out | 7 +
clipper/t/out/multx/test3.err | 2 +
clipper/t/out/multx/test3.out | 7 +
clipper/t/out/multx/test4.err | 5 +
clipper/t/out/multx/test4.out | 7 +
clipper/t/test-prep.pl | 79 +
clipper/testchrdex-speed.pl | 18 +
clipper/testchrdex.pl | 22 +
clipper/testsuf.pl | 11 +
clipper/tidx/Makefile | 33 +
clipper/tidx/README | 11 +
clipper/tidx/chr20.txt | 30738 +++++++++++++++++++
clipper/tidx/chr20.txt.tidx | Bin 0 -> 165025 bytes
{tidx => clipper/tidx}/fastq-lib.cpp | 0
{tidx => clipper/tidx}/fastq-lib.h | 0
clipper/tidx/foo.txt | 3 +
clipper/tidx/perl/Changes | 6 +
clipper/tidx/perl/MANIFEST | 32 +
clipper/tidx/perl/Makefile.PL | 39 +
clipper/tidx/perl/README | 41 +
clipper/tidx/perl/Tidx.xs | 32 +
{tidx => clipper/tidx/perl}/fastq-lib.cpp | 0
{tidx => clipper/tidx/perl}/fastq-lib.h | 0
clipper/tidx/perl/lib/Text/Tidx.pm | 172 +
clipper/tidx/perl/perlobject.map | 106 +
clipper/tidx/perl/ppport.h | 7063 +++++
clipper/tidx/perl/send2cpan | 28 +
clipper/tidx/perl/t/Text-Tidx.t | 40 +
clipper/tidx/perl/t/annot.txt | 862 +
clipper/tidx/perl/t/res1.txt | 1 +
clipper/tidx/perl/t/res2.txt | 1 +
clipper/tidx/perl/tidx-lib.cpp | 1 +
clipper/tidx/perl/tidx.cpp | 1 +
clipper/tidx/perl/tidx.h | 1 +
clipper/tidx/perl/typemap | 2 +
{tidx => clipper/tidx/perl}/utils.cpp | 0
{tidx => clipper/tidx/perl}/utils.h | 0
{tidx => clipper/tidx}/tidx-lib.cpp | 0
{tidx => clipper/tidx}/tidx.cpp | 0
{tidx => clipper/tidx}/tidx.h | 0
{tidx => clipper/tidx}/utils.cpp | 0
{tidx => clipper/tidx}/utils.h | 0
clipper/utils.cpp | 39 +
utils.h => clipper/utils.h | 0
clipper/varcall-matrix | 248 +
clipper/varcall.cpp | 2531 ++
clipper/xjoin | 546 +
clipper/zhead | 64 +
faidx.c | 437 -
kaln.c | 486 -
knetfile.c | 632 -
kprobaln.c | 280 -
kstring.c | 212 -
padding.c | 479 -
phase.c | 687 -
razf.c | 853 -
razip.c | 141 -
sam.c | 186 -
sam_header.c | 772 -
varcall.cpp | 1744 --
330 files changed, 91723 insertions(+), 11687 deletions(-)
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