[med-svn] [sra-sdk] branch upstream updated (05ef62f -> 82d7c33)
Andreas Tille
tille at debian.org
Wed Dec 30 07:52:55 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository sra-sdk.
from 05ef62f Imported Upstream version 2.4.2-1
new 82d7c33 Imported Upstream version 2.5.7
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:
.gitignore | 16 +-
GNU-license.txt | 674 ---
LICENSE | 66 +
Makefile | 13 +-
README | 53 +-
README-WINDOWS.txt | 144 -
README-build | 237 -
README-config.txt | 19 -
README-vdb-config.txt => README-vdb-config | 4 -
README-wget.txt | 35 -
README.md | 8 +-
USAGE | 162 -
build/MSVC/2010/abi-dump.vcxproj | 2 -
...d-filter-redact.vcxproj => align-cache.vcxproj} | 76 +-
build/MSVC/2010/align-info.vcxproj | 2 -
build/MSVC/2010/cache-mgr.vcxproj | 4 +-
...q-dump-ngs.vcxproj => dbgap-mount-demo.vcxproj} | 13 +-
build/MSVC/2010/dll-project.props | 59 -
build/MSVC/2010/exe-project.props | 70 +-
build/MSVC/2010/fastq-dump-ngs.vcxproj | 5 +-
build/MSVC/2010/fastq-dump.vcxproj | 2 -
build/MSVC/2010/fastq-loader.vcxproj | 6 +-
.../{kdbmeta.vcxproj => general-loader.vcxproj} | 16 +-
...llumina-diump.vcxproj => illumina-dump.vcxproj} | 0
build/MSVC/2010/kar.vcxproj | 2 -
build/MSVC/2010/kdbmeta.vcxproj | 2 -
build/MSVC/2010/lib-project.props | 68 +-
build/MSVC/2010/md5cp.vcxproj | 4 +-
build/MSVC/2010/prefetch.vcxproj | 5 +-
build/MSVC/2010/qual-recalib-stat.vcxproj | 4 -
build/MSVC/2010/rcexplain.vcxproj | 2 -
build/MSVC/2010/read-filter-redact.vcxproj | 2 -
...astq-dump-ngs.vcxproj => ref-variation.vcxproj} | 84 +-
build/MSVC/2010/sam-dump.vcxproj | 4 +-
build/MSVC/2010/schema-replace.vcxproj | 2 -
build/MSVC/2010/sff-dump.vcxproj | 2 -
build/MSVC/2010/sra-kar.vcxproj | 2 -
build/MSVC/2010/sra-pileup.vcxproj | 4 +-
build/MSVC/2010/sra-stat.vcxproj | 4 +-
build/MSVC/2010/sra-tools.sln | 70 +-
build/MSVC/2010/srapath.vcxproj | 2 -
.../{md5cp.vcxproj => test-align-info.vcxproj} | 23 +-
...tq-loader.vcxproj => test-fastq-loader.vcxproj} | 17 +-
...kdbmeta.vcxproj => test-general-loader.vcxproj} | 22 +-
build/MSVC/2010/test-sra-tools.sln | 66 +
build/MSVC/2010/test-sra.vcxproj | 2 -
...ema-replace.vcxproj => test-vcf-loader.vcxproj} | 21 +-
.../{fastq-dump-ngs.vcxproj => var-expand.vcxproj} | 84 +-
build/MSVC/2010/vdb-common.props | 92 +-
build/MSVC/2010/vdb-config.vcxproj | 9 +-
build/MSVC/2010/vdb-copy.vcxproj | 3 -
build/MSVC/2010/vdb-decrypt.vcxproj | 2 -
.../{vdb-validate.vcxproj => vdb-diff.vcxproj} | 9 +-
build/MSVC/2010/vdb-dump.vcxproj | 3 -
build/MSVC/2010/vdb-encrypt.vcxproj | 2 -
build/MSVC/2010/vdb-lock.vcxproj | 2 -
build/MSVC/2010/vdb-passwd.vcxproj | 2 -
build/MSVC/2010/vdb-unlock.vcxproj | 2 -
build/MSVC/2010/vdb-validate.vcxproj | 2 -
...{fastq-loader.vcxproj => wb-test-fastq.vcxproj} | 17 +-
build/Makefile.clang | 16 +-
build/Makefile.env | 29 +-
build/Makefile.gcc | 16 +-
build/Makefile.install | 56 +-
build/Makefile.linux | 3 +
build/Makefile.mac | 3 +
build/ld.linux.dlib.sh | 4 +-
build/ld.linux.exe.sh | 18 +-
build/ld.linux.gcc.sh | 5 +-
build/ld.mac.clang.sh | 7 +-
build/ld.mac.gcc.sh | 7 +-
build/ld.mac.slib.sh | 35 +-
configure | 6 +-
konfigure.perl | 1204 -----
os-arch.perl | 35 -
configure => setup/install | 10 +-
setup/install.perl | 1329 ++++++
setup/install.prl | 38 +
setup/konfigure.perl | 1717 +++++++
setup/os-arch.perl | 22 +
os-arch.pm => setup/os-arch.prl | 12 +-
package.pm => setup/package.prl | 48 +-
configure => setup/s/install | 12 +-
setup/s/os.prl | 2 +
test/Makefile | 38 +-
test/{ => align-info}/Makefile | 30 +-
test/fastq-loader/.gitignore | 1 +
test/fastq-loader/Makefile | 207 +
test/fastq-loader/expected/1.1.stdout | 31 +
test/fastq-loader/expected/1.2.stdout | 31 +
test/fastq-loader/expected/1.3.stderr | 4 +
test/fastq-loader/expected/1.3.stdout | 27 +
test/fastq-loader/expected/1.4.stdout | 90 +
test/fastq-loader/expected/10.0.stdout | 31 +
test/fastq-loader/expected/11.0.stdout | 31 +
test/fastq-loader/expected/11.1.stdout | 31 +
test/fastq-loader/expected/12.0.stdout | 60 +
test/fastq-loader/expected/12.1.stdout | 60 +
test/fastq-loader/expected/12.2.stdout | 31 +
test/fastq-loader/expected/2.1.1.stdout | 44 +
test/fastq-loader/expected/2.1.stdout | 60 +
test/fastq-loader/expected/2.5.stdout | 60 +
test/fastq-loader/expected/2.6.stdout | 31 +
test/fastq-loader/expected/2.7.stdout | 31 +
test/fastq-loader/expected/2.8.1.stdout | 60 +
test/fastq-loader/expected/2.8.stdout | 60 +
test/fastq-loader/expected/2.9.1.stderr | 4 +
test/fastq-loader/expected/2.9.stderr | 4 +
test/fastq-loader/expected/3.1.stdout | 120 +
test/fastq-loader/expected/4.2.stdout | 31 +
test/fastq-loader/expected/4.3.1.stderr | 14 +
test/fastq-loader/expected/4.4.stdout | 66 +
test/fastq-loader/expected/4.5.1.stderr | 8 +
test/fastq-loader/expected/4.5.stderr | 9 +
test/fastq-loader/expected/4.6.1.stderr | 3 +
test/fastq-loader/expected/4.6.stdout | 31 +
test/fastq-loader/expected/4.7.stderr | 2 +
test/fastq-loader/expected/5.0.stdout | 31 +
test/fastq-loader/expected/6.0.stdout | 390 ++
test/fastq-loader/expected/7.1.stdout | 60 +
test/fastq-loader/expected/7.2.stdout | 60 +
test/fastq-loader/expected/7.3.stdout | 60 +
test/fastq-loader/expected/8.0.stdout | 31 +
test/fastq-loader/expected/8.1.stderr | 5 +
test/fastq-loader/expected/9.0.stdout | 60 +
test/fastq-loader/input/1.1.fastq | 5 +
test/fastq-loader/input/1.2.fastq | 5 +
test/fastq-loader/input/1.3.fastq | 5 +
test/fastq-loader/input/1.4.fastq | 24 +
test/fastq-loader/input/10.0.fastq | 4 +
test/fastq-loader/input/11.0.1.fasta | 2 +
test/fastq-loader/input/11.0.2.fasta | 2 +
test/fastq-loader/input/11.1.1.fastq | 4 +
test/fastq-loader/input/11.1.2.fastq | 4 +
test/fastq-loader/input/12.0.fastq | 8 +
test/fastq-loader/input/12.1.fastq | 8 +
test/fastq-loader/input/12.2.fastq | 4 +
test/fastq-loader/input/2.1.1.fastq | 5 +
test/fastq-loader/input/2.1.fastq | 4 +
test/fastq-loader/input/2.2.fastq | 4 +
test/fastq-loader/input/2.3.fastq | 8 +
test/fastq-loader/input/2.4.fastq | 8 +
test/fastq-loader/input/2.5.fastq | 9 +
test/fastq-loader/input/2.6.fastq | 9 +
test/fastq-loader/input/2.7.fastq | 8 +
test/fastq-loader/input/2.8.1.fastq | 4 +
test/fastq-loader/input/2.8.fastq | 4 +
test/fastq-loader/input/2.9.1.fastq | 4 +
test/fastq-loader/input/2.9.fastq | 4 +
test/fastq-loader/input/3.1a.fastq | 8 +
test/fastq-loader/input/3.1b.fastq | 9 +
test/fastq-loader/input/3.2a.fastq | 8 +
test/fastq-loader/input/3.2b.fastq | 8 +
test/fastq-loader/input/3.3a.fastq | 8 +
test/fastq-loader/input/3.3b.fastq | 8 +
test/fastq-loader/input/4.4.fastq | 13 +
test/fastq-loader/input/4.5.1.fastq | 10 +
test/fastq-loader/input/4.5.fastq | 10 +
test/fastq-loader/input/4.fastq | 5 +
test/fastq-loader/input/5.0.fastq.gz | Bin 0 -> 139 bytes
test/fastq-loader/input/6.0.fastq | 52 +
test/fastq-loader/input/7.1.fastq | 9 +
test/fastq-loader/input/7.2.fastq | 8 +
test/fastq-loader/input/7.3.fastq | 8 +
test/fastq-loader/input/8.0.fastq | 9 +
test/fastq-loader/input/8.1.fastq | 17 +
test/fastq-loader/input/9.0.fastq | 16 +
test/fastq-loader/runtestcase.sh | 106 +
test/fastq-loader/test-fastq-loader.cpp | 215 +
test/fastq-loader/wb-test-fastq.cpp | 1376 ++++++
test/general-loader/.gitignore | 3 +
test/general-loader/Makefile | 194 +
test/general-loader/column01 | 3 +
test/general-loader/column02 | 3 +
test/general-loader/expected/1.stdout | 75 +
test/general-loader/expected/1override.stdout | 75 +
test/general-loader/expected/1packed.stdout | 75 +
test/general-loader/expected/2.stderr | 2 +
test/general-loader/expected/2packed.stderr | 2 +
test/general-loader/expected/3.stdout | 16 +
test/general-loader/expected/3packed.stdout | 16 +
test/general-loader/expected/4.stdout | 160 +
test/general-loader/expected/4packed.stdout | 160 +
test/general-loader/expected/5packed.stdout | 16 +
test/general-loader/expected/6.stdout | 1 +
test/general-loader/expected/6packed.stdout | 1 +
test/general-loader/makeinputs.cpp | 226 +
test/general-loader/runtestcase.sh | 108 +
test/general-loader/schema/.gitignore | 4 +
test/general-loader/test-general-loader.cpp | 1698 +++++++
test/general-loader/test-general-writer.cpp | 341 ++
.../general-loader/test-gw-dumper.cpp | 85 +-
test/general-loader/testsource.cpp | 758 +++
test/general-loader/testsource.hpp | 177 +
test/kget/.gitignore | 3 +
configure => test/kget/Makefile | 53 +-
{tools/cg-dump => test/network-test}/Makefile | 48 +-
test/network-test/network-test.c | 105 +
.../network-test/network-test.vers | 0
test/network-test/network-testing.c | 436 ++
.../network-test/network-testing.h | 12 +-
test/ngs-pileup/Makefile | 140 +
test/ngs-pileup/runtestcase.sh | 90 +
test/ngs-pileup/test-ngs-pileup.cpp | 177 +
test/ngs-pileup/valgrind.suppress | 6 +
test/only-remote-repository.kfg | 2 +
test/ref-variation/Makefile | 57 +
test/ref-variation/valgrind.suppress | 6 +
{tools/sra-dbcc => test/samline}/Makefile | 34 +-
test/samline/alig-gen.c | 604 +++
test/samline/cigar.c | 446 ++
.../line_token_iter.h => test/samline/cigar.h | 37 +-
test/samline/example.sh | 64 +
test/samline/refbases.c | 145 +
.../vtblcp-priv.h => test/samline/refbases.h | 9 +-
.../dump-idx.vers => test/samline/samline.vers | 0
test/tarballs/build.xml | 27 +
test/tarballs/test-tarballs.bat | 40 +
test/tarballs/test-tarballs.sh | 97 +
configure => test/vcf-loader/Makefile | 70 +-
test/vcf-loader/test-vcf-loader.cpp | 864 ++++
test/{ => vdb-dump}/Makefile | 29 +-
test/vdb-dump/SRR056386 | Bin 0 -> 14505 bytes
test/vdb-dump/expected/1.0.stdout | 1 +
test/vdb-dump/expected/1.1.stdout | 1 +
test/vschema/Makefile | 115 +
.../vschema/bio-end/bio-end-excl.vschema | 31 +-
.../vschema/bio-end/bio-end-incl.vschema | 31 +-
test/vschema/bio-end/expected/excl-1.stdout | 5 +
test/vschema/bio-end/expected/excl-2.stdout | 5 +
test/vschema/bio-end/expected/excl-3.stdout | 5 +
test/vschema/bio-end/expected/excl-4.stdout | 5 +
test/vschema/bio-end/expected/incl-1.stdout | 5 +
test/vschema/bio-end/makeinputs.cpp | 129 +
test/vschema/idx-text/checklookup.cpp | 323 ++
test/vschema/idx-text/expected/ci-1.stdout | 15 +
test/vschema/idx-text/expected/ci-2.stdout | 18 +
test/vschema/idx-text/expected/ci-3.stdout | 12 +
test/vschema/idx-text/expected/ci-4.stdout | 12 +
test/vschema/idx-text/expected/cs-1.stdout | 18 +
test/vschema/idx-text/expected/cs-2.stdout | 18 +
test/vschema/idx-text/idx-text.vschema | 105 +
test/vschema/idx-text/makeinputs.cpp | 148 +
test/vschema/runtestcase.sh | 126 +
tools/.gitignore | 3 +
tools/Makefile | 66 +-
tools/agp-load/AGP.py | 668 +++
tools/agp-load/agp-load.py | 173 +
tools/agp-load/agp.vschema | 45 +
tools/agp-load/eutils.py | 112 +
tools/{vtblcp => align-cache}/Makefile | 34 +-
tools/align-cache/align-cache.cpp | 557 +++
.../dump-idx.vers => align-cache/align-cache.vers} | 0
tools/align-cache/align-cache.vers.h | 1 +
tools/align-cache/helper.cpp | 923 ++++
tools/align-cache/helper.h | 390 ++
tools/align-info/align-info.c | 20 +-
tools/align-info/align-info.vers | 2 +-
tools/align-info/align-info.vers.h | 2 +-
tools/bam-loader/Globals.h | 1 +
tools/bam-loader/Makefile | 32 +-
tools/bam-loader/bam-load.3.vers | 1 -
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/bam-loader.c | 63 +-
tools/bam-loader/bam-loader3.c | 1028 -----
tools/bam-loader/bam.c | 4085 ++++++++++++++++
tools/bam-loader/bam.h | 632 +++
tools/bam-loader/config-file.cpp | 195 +
.../key_value.h => bam-loader/config-file.hpp} | 73 +-
tools/bam-loader/fasta-file.cpp | 257 ++
.../idx-mapping.h => bam-loader/fasta-file.hpp} | 68 +-
tools/bam-loader/loader-imp.c | 1426 +++---
tools/bam-loader/loader-imp3.c | 369 --
tools/bam-loader/mem-bank.cpp | 477 ++
.../fastq-reader.h => bam-loader/mem-bank.h} | 29 +-
tools/bam-loader/reference-writer.c | 214 +-
tools/bam-loader/reference-writer.h | 12 +-
tools/bam-loader/sequence-writer.c | 24 +-
tools/cache-mgr/cache-mgr.c | 64 +-
tools/cache-mgr/cache-mgr.vers | 2 +-
tools/cache-mgr/cache-mgr.vers.h | 2 +-
tools/ccextract/Makefile | 25 +-
tools/ccextract/ccextract.c | 16 +-
tools/ccextract/ccextract.vers | 2 +-
tools/cg-dump/cg-dump.c | 1563 -------
tools/cg-dump/cg-dump.vers | 1 -
tools/cg-dump/last_rowid.c | 353 --
tools/cg-dump/line_token_iter.c | 148 -
tools/cg-dump/num-gen.c | 848 ----
tools/cg-dump/num-gen.h | 225 -
tools/cg-dump/progressbar.c | 140 -
tools/cg-dump/progressbar.h | 70 -
tools/cg-dump/sg_lookup.c | 277 --
tools/cg-load/Makefile | 5 +-
tools/cg-load/cg-load.c | 281 +-
tools/cg-load/cg-load.vers | 2 +-
tools/cg-load/defs.h | 41 +-
tools/cg-load/f1_3.c | 1 +
tools/cg-load/f1_5.c | 2 +-
tools/cg-load/{f1_5.c => f1_7.c} | 39 +-
tools/cg-load/f2_0.c | 18 +-
tools/cg-load/f2_2.c | 4 +-
tools/cg-load/f2_5.c | 98 +
tools/cg-load/factory-evidence-dnbs.c | 290 +-
tools/cg-load/factory-evidence-dnbs.h | 3 +
tools/cg-load/factory-evidence-intervals.c | 100 +-
tools/cg-load/factory-evidence-intervals.h | 3 +
tools/cg-load/factory-file.h | 4 +
tools/cg-load/factory-mappings.c | 213 +-
tools/cg-load/factory-mappings.h | 3 +
tools/cg-load/factory-reads.c | 246 +-
tools/cg-load/factory-reads.h | 3 +
tools/cg-load/factory-tag-lfr.c | 183 +-
tools/cg-load/factory-tag-lfr.h | 6 +-
tools/cg-load/file-version-factory.c | 7 +-
tools/cg-load/file.c | 149 +-
tools/cg-load/file.h | 1 +
tools/{vdb-dump/vdb_info.h => cg-load/formats.c} | 37 +-
tools/{vtblcp/vtblcp-priv.h => cg-load/formats.h} | 19 +-
tools/cg-load/writer-algn.c | 128 +-
tools/cg-load/writer-algn.h | 3 +-
tools/cg-load/writer-evidence-dnbs.c | 56 +-
tools/cg-load/writer-evidence-dnbs.h | 19 +-
tools/cg-load/writer-evidence-intervals.c | 25 +-
tools/cg-load/writer-seq.c | 36 +-
tools/cg-load/writer-seq.h | 12 +-
tools/check-blob-size/check-blob-size.c | 332 --
tools/check-blob-size/check-blob-size.vers | 1 -
tools/copycat/Makefile | 28 +-
tools/copycat/cccat.c | 12 +-
tools/copycat/ccsra.c | 2 +-
tools/copycat/cctree.c | 6 +-
tools/copycat/copycat.c | 14 +-
tools/copycat/copycat.vers | 2 +-
tools/{workspace => dbgap-mount}/Makefile | 82 +-
tools/dbgap-mount/demo.c | 360 ++
tools/dbgap-mount/demo.mkfg | 47 +
.../sra-gui/sra-gui.vers => dbgap-mount/demo.vers} | 0
tools/dbgap-mount/demo.vers.h | 1 +
tools/deseq/csra-trim.vers | 1 -
tools/deseq/deseq.c | 521 ---
tools/fastq-dump/Makefile | 18 +-
tools/fastq-dump/args.cpp | 12 +-
tools/fastq-dump/args.hpp | 2 +-
tools/fastq-dump/fastq-dump.cpp | 146 +-
tools/fastq-dump/fastq-dump.vers | 2 +-
tools/fastq-dump/koutstream | 73 +-
tools/fastq-loader/Makefile | 13 +-
tools/fastq-loader/fastq-grammar.c | 714 +--
tools/fastq-loader/fastq-grammar.y | 224 +-
tools/fastq-loader/fastq-lex.c | 749 ++-
tools/fastq-loader/fastq-lex.l | 20 +-
tools/fastq-loader/fastq-loader.c | 80 +-
tools/fastq-loader/fastq-parse.h | 50 +-
tools/fastq-loader/fastq-reader.c | 45 +-
tools/fastq-loader/fastq-reader.h | 9 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/fastq-loader/latf-load.vers.h | 2 +-
tools/fastq-loader/loader-imp.c | 19 +-
tools/fastq-loader/parsing_rules.txt | 93 +
tools/fix-run-stat/fix-run-stat.c | 355 --
tools/fix-run-stat/fix-run-stat.vers | 1 -
tools/fuse/Makefile | 37 +
tools/fuse/directory.c | 8 +-
tools/fuse/remote-cache.c | 12 +-
tools/fuse/remote-directory.c | 4 +-
tools/fuse/remote-fuser.vers | 2 +-
tools/fuse/sra-fuser-test.vers | 2 +-
tools/fuse/sra-fuser-test.vers.h | 2 +-
tools/fuse/sra-fuser.vers | 2 +-
tools/fuse/sra-list.c | 6 +-
tools/fuse/sra-makeidx.c | 6 +-
tools/fuse/sra-makeidx.vers | 2 +-
tools/fuse/tar-list.c | 4 +-
tools/fuse/unix/sra-fuser-sys.c | 37 +-
tools/{meta-sync => general-loader}/Makefile | 100 +-
tools/general-loader/database-loader.cpp | 895 ++++
tools/general-loader/general-loader.cpp | 223 +
tools/general-loader/general-loader.hpp | 243 +
tools/general-loader/general-loader.vers | 1 +
tools/general-loader/general-loader.vers.h | 1 +
tools/general-loader/general-writer.cpp | 1172 +++++
tools/general-loader/general-writer.h | 1081 +++++
tools/general-loader/general-writer.hpp | 210 +
tools/general-loader/gw-dumper.cpp | 1785 +++++++
tools/general-loader/libgeneral-writer.vers | 1 +
tools/general-loader/main.cpp | 246 +
tools/general-loader/protocol-parser.cpp | 1048 +++++
tools/general-loader/utf8-like-int-codec.c | 687 +++
.../utf8-like-int-codec.h} | 63 +-
tools/kar/kar.c | 21 +-
tools/kar/kar.vers | 2 +-
tools/kar/kar.vers.h | 2 +-
tools/kar/sra-kar.c | 10 +-
tools/kar/sra-kar.vers | 2 +-
tools/kar/sra-kar.vers.h | 2 +-
tools/keyring-srv/keyring-data.c | 8 +-
tools/keyring-srv/keyring-srv.vers | 2 +-
tools/{sra-dbcc => kget}/Makefile | 31 +-
tools/kget/kget.c | 688 +++
tools/{fuse/dump-idx.vers => kget/kget.vers} | 0
tools/kqsh/kqsh.c | 2 +-
tools/kqsh/kqsh.vers | 2 +-
tools/meta-sync/meta-sync.c | 1517 ------
tools/meta-sync/meta-sync.pl | 41 -
tools/meta-sync/meta-sync.vers | 1 -
tools/nenctool/nenctest.c | 10 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.c | 12 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/nencvalid.c | 9 +-
tools/nencvalid/nencvalid.vers | 2 +-
tools/{fix-run-stat => ngs-pileup}/Makefile | 46 +-
tools/ngs-pileup/main.cpp | 164 +
tools/ngs-pileup/ngs-pileup.cpp | 206 +
tools/ngs-pileup/ngs-pileup.hpp | 97 +
.../sra-gui.vers => ngs-pileup/ngs-pileup.vers} | 0
tools/ngs-pileup/ngs-pileup.vers.h | 1 +
tools/pacbio-load/Makefile | 8 +-
tools/pacbio-load/pacbio-load.vers | 2 +-
tools/pacbio-load/pl-consensus.c | 227 +-
tools/pacbio-load/pl-context.c | 4 +-
tools/pacbio-load/pl-regions.c | 4 +-
tools/pacbio-load/pl-tools.c | 22 +-
tools/{deseq => pileup-stats}/Makefile | 47 +-
tools/pileup-stats/pileup-stats.cpp | 719 +++
tools/pileup-stats/pileup-stats.vers | 1 +
tools/pore-load/GeneralWriter.py | 312 ++
tools/pore-load/README.md | 10 +
tools/pore-load/pore-load.py | 406 ++
tools/prefetch/Makefile | 3 +-
tools/prefetch/kfile-no-q.c | 215 +
.../loader-imp3.h => prefetch/kfile-no-q.h} | 26 +-
tools/prefetch/prefetch.c | 1020 +++-
tools/prefetch/prefetch.vers | 2 +-
tools/prefetch/prefetch.vers.h | 2 +-
tools/qual-recal/Makefile | 101 -
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