[med-svn] [ea-utils] branch master updated (3ba9b90 -> 599e900)
Andreas Tille
tille at debian.org
Mon May 8 17:17:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository ea-utils.
from 3ba9b90 UPload to unstable
new 1e8a6c3 Point watch file to github since upstream is now tagging releases
new 90501c6 Adapt Files-Excluded to new source tarball layout
new 0bd5483 New upstream version 1.04.807+dfsg
new 599e900 Merge tag 'upstream/1.04.807+dfsg'
The 4 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 +
debian/changelog | 6 +
debian/copyright | 6 +-
debian/watch | 5 +-
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 --
333 files changed, 91735 insertions(+), 11692 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
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copy {tidx => clipper/tidx}/fastq-lib.h (100%)
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copy {tidx => clipper/tidx/perl}/utils.h (100%)
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rename {tidx => clipper/tidx}/tidx.cpp (100%)
rename {tidx => clipper/tidx}/tidx.h (100%)
rename {tidx => clipper/tidx}/utils.cpp (100%)
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