[med-svn] [ea-utils] branch upstream updated (8ad9ba2 -> 0bd5483)
Andreas Tille
tille at debian.org
Mon May 8 17:17:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository ea-utils.
from 8ad9ba2 Imported Upstream version 1.1.2+dfsg
new 0bd5483 New upstream version 1.04.807+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:
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(-)
create mode 100644 README.md
delete mode 100644 bam.c
delete mode 100644 bam_aux.c
delete mode 100644 bam_cat.c
delete mode 100644 bam_import.c
delete mode 100644 bam_index.c
delete mode 100644 bam_lpileup.c
delete mode 100644 bam_md.c
delete mode 100644 bam_pileup.c
delete mode 100644 bam_reheader.c
delete mode 100644 bam_sort.c
delete mode 100644 bedidx.c
delete mode 100644 bgzf.c
rename CHANGES => clipper/CHANGES (68%)
create mode 100644 clipper/Chrdex.pm
create mode 100644 clipper/Grun.pm
create mode 100644 clipper/HyperLevelDB/.gitignore
create mode 100644 clipper/HyperLevelDB/.tarballignore
create mode 100644 clipper/HyperLevelDB/AUTHORS
create mode 100644 clipper/HyperLevelDB/LICENSE
create mode 100644 clipper/HyperLevelDB/Makefile.am
create mode 100644 clipper/HyperLevelDB/NEWS
create mode 100644 clipper/HyperLevelDB/README
create mode 100644 clipper/HyperLevelDB/TODO
create mode 100644 clipper/HyperLevelDB/benchmark.cc
create mode 100644 clipper/HyperLevelDB/configure.ac
create mode 100644 clipper/HyperLevelDB/db/autocompact_test.cc
create mode 100644 clipper/HyperLevelDB/db/builder.cc
create mode 100644 clipper/HyperLevelDB/db/builder.h
create mode 100644 clipper/HyperLevelDB/db/c.cc
create mode 100644 clipper/HyperLevelDB/db/c_test.c
create mode 100644 clipper/HyperLevelDB/db/corruption_test.cc
create mode 100644 clipper/HyperLevelDB/db/db_bench.cc
create mode 100644 clipper/HyperLevelDB/db/db_impl.cc
create mode 100644 clipper/HyperLevelDB/db/db_impl.h
create mode 100644 clipper/HyperLevelDB/db/db_iter.cc
create mode 100644 clipper/HyperLevelDB/db/db_iter.h
create mode 100644 clipper/HyperLevelDB/db/db_test.cc
create mode 100644 clipper/HyperLevelDB/db/dbformat.cc
create mode 100644 clipper/HyperLevelDB/db/dbformat.h
create mode 100644 clipper/HyperLevelDB/db/dbformat_test.cc
create mode 100644 clipper/HyperLevelDB/db/filename.cc
create mode 100644 clipper/HyperLevelDB/db/filename.h
create mode 100644 clipper/HyperLevelDB/db/filename_test.cc
create mode 100644 clipper/HyperLevelDB/db/leveldb_main.cc
create mode 100644 clipper/HyperLevelDB/db/log_format.h
create mode 100644 clipper/HyperLevelDB/db/log_reader.cc
create mode 100644 clipper/HyperLevelDB/db/log_reader.h
create mode 100644 clipper/HyperLevelDB/db/log_test.cc
create mode 100644 clipper/HyperLevelDB/db/log_writer.cc
create mode 100644 clipper/HyperLevelDB/db/log_writer.h
create mode 100644 clipper/HyperLevelDB/db/memtable.cc
create mode 100644 clipper/HyperLevelDB/db/memtable.h
create mode 100644 clipper/HyperLevelDB/db/repair.cc
create mode 100644 clipper/HyperLevelDB/db/replay_iterator.cc
create mode 100644 clipper/HyperLevelDB/db/replay_iterator.h
create mode 100644 clipper/HyperLevelDB/db/skiplist.h
create mode 100644 clipper/HyperLevelDB/db/skiplist_test.cc
create mode 100644 clipper/HyperLevelDB/db/snapshot.h
create mode 100644 clipper/HyperLevelDB/db/table_cache.cc
create mode 100644 clipper/HyperLevelDB/db/table_cache.h
create mode 100644 clipper/HyperLevelDB/db/version_edit.cc
create mode 100644 clipper/HyperLevelDB/db/version_edit.h
create mode 100644 clipper/HyperLevelDB/db/version_edit_test.cc
create mode 100644 clipper/HyperLevelDB/db/version_set.cc
create mode 100644 clipper/HyperLevelDB/db/version_set.h
create mode 100644 clipper/HyperLevelDB/db/version_set_test.cc
create mode 100644 clipper/HyperLevelDB/db/write_batch.cc
create mode 100644 clipper/HyperLevelDB/db/write_batch_internal.h
create mode 100644 clipper/HyperLevelDB/db/write_batch_test.cc
create mode 100644 clipper/HyperLevelDB/doc/bench/db_bench_sqlite3.cc
create mode 100644 clipper/HyperLevelDB/doc/bench/db_bench_tree_db.cc
create mode 100644 clipper/HyperLevelDB/doc/benchmark.html
create mode 100644 clipper/HyperLevelDB/doc/doc.css
create mode 100644 clipper/HyperLevelDB/doc/impl.html
create mode 100644 clipper/HyperLevelDB/doc/index.html
create mode 100644 clipper/HyperLevelDB/doc/log_format.txt
create mode 100644 clipper/HyperLevelDB/doc/table_format.txt
create mode 100644 clipper/HyperLevelDB/helpers/memenv/memenv.cc
create mode 100644 clipper/HyperLevelDB/helpers/memenv/memenv.h
create mode 100644 clipper/HyperLevelDB/helpers/memenv/memenv_test.cc
create mode 100644 clipper/HyperLevelDB/hyperleveldb.upack.in
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/c.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/cache.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/comparator.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/db.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/env.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/filter_policy.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/iterator.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/options.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/replay_iterator.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/slice.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/status.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/table.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/table_builder.h
create mode 100644 clipper/HyperLevelDB/include/hyperleveldb/write_batch.h
create mode 100644 clipper/HyperLevelDB/issues/issue178_test.cc
create mode 100644 clipper/HyperLevelDB/issues/issue200_test.cc
create mode 100644 clipper/HyperLevelDB/leveldb-verify.cc
create mode 100644 clipper/HyperLevelDB/libhyperleveldb.pc.in
create mode 100644 clipper/HyperLevelDB/m4/ax_check_compile_flag.m4
create mode 100644 clipper/HyperLevelDB/port/README
create mode 100644 clipper/HyperLevelDB/port/atomic_pointer.h
create mode 100644 clipper/HyperLevelDB/port/port.h
create mode 100644 clipper/HyperLevelDB/port/port_example.h
create mode 100644 clipper/HyperLevelDB/port/port_posix.cc
create mode 100644 clipper/HyperLevelDB/port/port_posix.h
create mode 100644 clipper/HyperLevelDB/port/thread_annotations.h
create mode 100644 clipper/HyperLevelDB/port/win/stdint.h
create mode 100644 clipper/HyperLevelDB/table/block.cc
create mode 100644 clipper/HyperLevelDB/table/block.h
create mode 100644 clipper/HyperLevelDB/table/block_builder.cc
create mode 100644 clipper/HyperLevelDB/table/block_builder.h
create mode 100644 clipper/HyperLevelDB/table/filter_block.cc
create mode 100644 clipper/HyperLevelDB/table/filter_block.h
create mode 100644 clipper/HyperLevelDB/table/filter_block_test.cc
create mode 100644 clipper/HyperLevelDB/table/format.cc
create mode 100644 clipper/HyperLevelDB/table/format.h
create mode 100644 clipper/HyperLevelDB/table/iterator.cc
create mode 100644 clipper/HyperLevelDB/table/iterator_wrapper.h
create mode 100644 clipper/HyperLevelDB/table/merger.cc
create mode 100644 clipper/HyperLevelDB/table/merger.h
create mode 100644 clipper/HyperLevelDB/table/table.cc
create mode 100644 clipper/HyperLevelDB/table/table_builder.cc
create mode 100644 clipper/HyperLevelDB/table/table_test.cc
create mode 100644 clipper/HyperLevelDB/table/two_level_iterator.cc
create mode 100644 clipper/HyperLevelDB/table/two_level_iterator.h
create mode 100644 clipper/HyperLevelDB/util/arena.cc
create mode 100644 clipper/HyperLevelDB/util/arena.h
create mode 100644 clipper/HyperLevelDB/util/arena_test.cc
create mode 100644 clipper/HyperLevelDB/util/bloom.cc
create mode 100644 clipper/HyperLevelDB/util/bloom_test.cc
create mode 100644 clipper/HyperLevelDB/util/cache.cc
create mode 100644 clipper/HyperLevelDB/util/cache_test.cc
create mode 100644 clipper/HyperLevelDB/util/coding.cc
create mode 100644 clipper/HyperLevelDB/util/coding.h
create mode 100644 clipper/HyperLevelDB/util/coding_test.cc
create mode 100644 clipper/HyperLevelDB/util/comparator.cc
create mode 100644 clipper/HyperLevelDB/util/crc32c.cc
create mode 100644 clipper/HyperLevelDB/util/crc32c.h
create mode 100644 clipper/HyperLevelDB/util/crc32c_test.cc
create mode 100644 clipper/HyperLevelDB/util/env.cc
create mode 100644 clipper/HyperLevelDB/util/env_posix.cc
create mode 100644 clipper/HyperLevelDB/util/env_test.cc
create mode 100644 clipper/HyperLevelDB/util/filter_policy.cc
create mode 100644 clipper/HyperLevelDB/util/hash.cc
create mode 100644 clipper/HyperLevelDB/util/hash.h
create mode 100644 clipper/HyperLevelDB/util/histogram.cc
create mode 100644 clipper/HyperLevelDB/util/histogram.h
create mode 100644 clipper/HyperLevelDB/util/logging.cc
create mode 100644 clipper/HyperLevelDB/util/logging.h
create mode 100644 clipper/HyperLevelDB/util/mutexlock.h
create mode 100644 clipper/HyperLevelDB/util/options.cc
create mode 100644 clipper/HyperLevelDB/util/posix_logger.h
create mode 100644 clipper/HyperLevelDB/util/random.h
create mode 100644 clipper/HyperLevelDB/util/status.cc
create mode 100644 clipper/HyperLevelDB/util/testharness.cc
create mode 100644 clipper/HyperLevelDB/util/testharness.h
create mode 100644 clipper/HyperLevelDB/util/testutil.cc
create mode 100644 clipper/HyperLevelDB/util/testutil.h
rename Makefile => clipper/Makefile (70%)
rename README => clipper/README (98%)
create mode 100644 clipper/affy-csv-to-bed.pl
create mode 100644 clipper/affy-liftover.pl
create mode 100644 clipper/aggregate-results-by-gene.pl
rename alc => clipper/alc (100%)
create mode 100644 clipper/align-sw.cpp
create mode 100644 clipper/bam-filter.cpp
create mode 100644 clipper/bowtie-gzip.patch
create mode 100755 clipper/bwa-to-bowtie
create mode 100755 clipper/check-clipper.sh
create mode 100755 clipper/contig-stats
create mode 100644 clipper/count-ambig.cpp
create mode 100755 clipper/debug
rename determine-phred => clipper/determine-phred (100%)
create mode 100644 clipper/ea-bcl2fastq.cpp
copy ea-utils.spec => clipper/ea-utils.spec (98%)
rename ea-utils.spec => clipper/ea-utils.spex (97%)
create mode 100755 clipper/fasta-qual-to-fastq
rename fastq-clipper.c => clipper/fastq-clipper.cpp (100%)
rename fastq-join.c => clipper/fastq-join.cpp (90%)
create mode 100644 clipper/fastq-join.t
rename fastq-lib.cpp => clipper/fastq-lib.cpp (74%)
rename fastq-lib.h => clipper/fastq-lib.h (96%)
rename fastq-mcf.c => clipper/fastq-mcf.cpp (94%)
rename fastq-multx.c => clipper/fastq-multx.cpp (84%)
rename fastq-stats.cpp => clipper/fastq-stats.cpp (99%)
create mode 100755 clipper/fastq-to-fasta
rename fastx-graph => clipper/fastx-graph (100%)
rename gcModel.c => clipper/gcModel.cpp (98%)
rename gcModel.h => clipper/gcModel.h (74%)
create mode 100755 clipper/getgenbankannot
create mode 100644 clipper/getline.c
create mode 100755 clipper/gff2gtf
create mode 100755 clipper/grun
rename gtf2bed => clipper/gtf2bed (87%)
create mode 100644 clipper/install-bamtools.sh
create mode 100755 clipper/master-barcodes.txt
create mode 100755 clipper/merge-fifo
create mode 100644 clipper/mirna-quant.cpp
create mode 100644 clipper/mixfastqs.pl
create mode 100755 clipper/multx.sh
create mode 100644 clipper/pbi-clean.cpp
create mode 100755 clipper/qsh
create mode 100755 clipper/qsub
rename randomFQ => clipper/randomFQ (100%)
rename sam-stats.cpp => clipper/sam-stats.cpp (95%)
create mode 100755 clipper/sam-stats.pl
create mode 100644 clipper/seqsig.cpp
create mode 100755 clipper/t/in/join/phred.1.fq
create mode 100755 clipper/t/in/join/phred.2.fq
create mode 100644 clipper/t/in/join/test-m1.fq
create mode 100644 clipper/t/in/join/test-m2.fq
create mode 100644 clipper/t/in/join/test-ov-a.1.fq
create mode 100644 clipper/t/in/join/test-ov-a.2.fq
create mode 100644 clipper/t/in/join/test-ov-b.1.fq
create mode 100644 clipper/t/in/join/test-ov-b.2.fq
create mode 100644 clipper/t/in/mcf/adap.fa
create mode 100644 clipper/t/in/mcf/count.fq
create mode 100644 clipper/t/in/mcf/test-mcf-dup.fq
create mode 100644 clipper/t/in/mcf/test.fa
create mode 100644 clipper/t/in/mcf/test1.fq
create mode 100644 clipper/t/in/mcf/test2.fq
create mode 100644 clipper/t/in/mcf/test3.fq
create mode 100644 clipper/t/in/mcf/test4.fq1
create mode 100644 clipper/t/in/mcf/test4.fq2
create mode 100644 clipper/t/in/mcf/test5.fq
create mode 100755 clipper/t/in/multx/master-barcodes.txt
create mode 100644 clipper/t/in/multx/mxtest-h_1.fastq
create mode 100644 clipper/t/in/multx/mxtest-h_2.fastq
create mode 100644 clipper/t/in/multx/mxtest_1.fastq
create mode 100644 clipper/t/in/multx/mxtest_2.fastq
create mode 100644 clipper/t/in/multx/mxtest_3.fastq
create mode 100644 clipper/t/join.t
create mode 100644 clipper/t/mcf.t
create mode 100644 clipper/t/multx.t
create mode 100644 clipper/t/out/join/test-m.join
create mode 100644 clipper/t/out/join/test-m.out
create mode 100644 clipper/t/out/join/test-nov-a.join
create mode 100644 clipper/t/out/join/test-nov-a.out
create mode 100644 clipper/t/out/join/test-nov-b.join
create mode 100644 clipper/t/out/join/test-nov-b.out
create mode 100644 clipper/t/out/join/test-ov-a.join
create mode 100644 clipper/t/out/join/test-ov-a.out
create mode 100644 clipper/t/out/join/test-ov-b.join
create mode 100644 clipper/t/out/join/test-ov-b.out
create mode 100644 clipper/t/out/join/test-phred.join
create mode 100644 clipper/t/out/join/test-phred.out
create mode 100644 clipper/t/out/mcf/test1.err
create mode 100644 clipper/t/out/mcf/test1.out
create mode 100644 clipper/t/out/mcf/test2.err
create mode 100644 clipper/t/out/mcf/test2.out
create mode 100644 clipper/t/out/mcf/test3.err
create mode 100644 clipper/t/out/mcf/test3.out
create mode 100644 clipper/t/out/mcf/test4.err
create mode 100644 clipper/t/out/mcf/test4.out1
create mode 100644 clipper/t/out/mcf/test4.out2
create mode 100644 clipper/t/out/mcf/test5.err
create mode 100644 clipper/t/out/mcf/test5.out
create mode 100644 clipper/t/out/mcf/test6.err
create mode 100644 clipper/t/out/mcf/test6.out.gz
create mode 100644 clipper/t/out/mcf/test7.err
create mode 100644 clipper/t/out/mcf/test7.out
create mode 100644 clipper/t/out/mcf/test8.err
create mode 100644 clipper/t/out/mcf/test8.out
create mode 100644 clipper/t/out/mcf/test9.err
create mode 100644 clipper/t/out/mcf/test9.out
create mode 100644 clipper/t/out/multx/test1.err
create mode 100644 clipper/t/out/multx/test1.out
create mode 100644 clipper/t/out/multx/test2.err
create mode 100644 clipper/t/out/multx/test2.out
create mode 100644 clipper/t/out/multx/test3.err
create mode 100644 clipper/t/out/multx/test3.out
create mode 100644 clipper/t/out/multx/test4.err
create mode 100644 clipper/t/out/multx/test4.out
create mode 100644 clipper/t/test-prep.pl
create mode 100644 clipper/testchrdex-speed.pl
create mode 100644 clipper/testchrdex.pl
create mode 100644 clipper/testsuf.pl
create mode 100644 clipper/tidx/Makefile
create mode 100644 clipper/tidx/README
create mode 100644 clipper/tidx/chr20.txt
create mode 100644 clipper/tidx/chr20.txt.tidx
copy {tidx => clipper/tidx}/fastq-lib.cpp (100%)
copy {tidx => clipper/tidx}/fastq-lib.h (100%)
create mode 100644 clipper/tidx/foo.txt
create mode 100644 clipper/tidx/perl/Changes
create mode 100644 clipper/tidx/perl/MANIFEST
create mode 100644 clipper/tidx/perl/Makefile.PL
create mode 100644 clipper/tidx/perl/README
create mode 100644 clipper/tidx/perl/Tidx.xs
rename {tidx => clipper/tidx/perl}/fastq-lib.cpp (100%)
rename {tidx => clipper/tidx/perl}/fastq-lib.h (100%)
create mode 100644 clipper/tidx/perl/lib/Text/Tidx.pm
create mode 100644 clipper/tidx/perl/perlobject.map
create mode 100644 clipper/tidx/perl/ppport.h
create mode 100755 clipper/tidx/perl/send2cpan
create mode 100644 clipper/tidx/perl/t/Text-Tidx.t
create mode 100644 clipper/tidx/perl/t/annot.txt
create mode 100644 clipper/tidx/perl/t/res1.txt
create mode 100644 clipper/tidx/perl/t/res2.txt
create mode 120000 clipper/tidx/perl/tidx-lib.cpp
create mode 120000 clipper/tidx/perl/tidx.cpp
create mode 120000 clipper/tidx/perl/tidx.h
create mode 100644 clipper/tidx/perl/typemap
copy {tidx => clipper/tidx/perl}/utils.cpp (100%)
copy {tidx => clipper/tidx/perl}/utils.h (100%)
rename {tidx => clipper/tidx}/tidx-lib.cpp (100%)
rename {tidx => clipper/tidx}/tidx.cpp (100%)
rename {tidx => clipper/tidx}/tidx.h (100%)
rename {tidx => clipper/tidx}/utils.cpp (100%)
rename {tidx => clipper/tidx}/utils.h (100%)
create mode 100644 clipper/utils.cpp
rename utils.h => clipper/utils.h (100%)
create mode 100755 clipper/varcall-matrix
create mode 100644 clipper/varcall.cpp
create mode 100644 clipper/xjoin
create mode 100755 clipper/zhead
delete mode 100644 faidx.c
delete mode 100644 kaln.c
delete mode 100644 knetfile.c
delete mode 100644 kprobaln.c
delete mode 100644 kstring.c
delete mode 100644 padding.c
delete mode 100644 phase.c
delete mode 100644 razf.c
delete mode 100644 razip.c
delete mode 100644 sam.c
delete mode 100644 sam_header.c
delete mode 100644 varcall.cpp
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ea-utils.git
More information about the debian-med-commit
mailing list