[med-svn] [sra-sdk] branch master updated (eb84f38 -> 4dd6dac)
Andreas Tille
tille at debian.org
Fri Oct 24 12:53:44 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sra-sdk.
from eb84f38 Renamed upstream -> upstream/metadata.
new 8da0436 New upstream version; d/watch points to github; d/copyright: no need to exclude any files any more
new 6d0c86f Imported Upstream version 2.4.2-1
new 7991ab2 Merge tag 'upstream/2.4.2-1'
new adce942 cme fix dpkg-control
new 0f20a64 Adapt patches
new 4dd6dac TODO: package ngs-sdk (https://github.com/ncbi/ngs)
The 6 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 | 5 +-
CHANGES | 30 +
GNU-license.txt | 674 +
Makefile | 49 +-
README | 21 +
README-blastn | 133 +
README-build | 237 +
README-build.txt | 239 -
README-config.txt | 51 +-
README-vdb-config.txt | 119 +
README-wget.txt | 35 +
README.md | 33 +
USAGE | 162 +
build/.gitignore | 5 +
build/BUILD.linux | 1 -
build/BUILD.mac | 1 -
build/BUILD.win | 1 -
build/COMP.linux | 1 -
build/COMP.mac | 1 -
build/COMP.win | 1 -
build/LNKG.linux | 1 -
build/LNKG.mac | 1 -
build/LNKG.win | 1 -
build/MSVC/2010/.gitignore | 5 +
build/MSVC/2010/abi-dump.vcxproj | 38 +
build/MSVC/2010/align-info.vcxproj | 40 +
build/MSVC/2010/cache-mgr.vcxproj | 40 +
build/MSVC/2010/dll-project.props | 90 +
build/MSVC/2010/exe-project.props | 104 +
build/MSVC/2010/fastq-dump-ngs.vcxproj | 44 +
build/MSVC/2010/fastq-dump.vcxproj | 42 +
build/MSVC/2010/fastq-loader.vcxproj | 46 +
build/MSVC/2010/illumina-diump.vcxproj | 43 +
build/MSVC/2010/kar.vcxproj | 40 +
build/MSVC/2010/kdbmeta.vcxproj | 40 +
build/MSVC/2010/lib-project.props | 96 +
build/MSVC/2010/md5cp.vcxproj | 39 +
build/MSVC/2010/prefetch.vcxproj | 40 +
build/MSVC/2010/qual-recalib-stat.vcxproj | 50 +
build/MSVC/2010/rcexplain.vcxproj | 40 +
build/MSVC/2010/read-filter-redact.vcxproj | 40 +
build/MSVC/2010/sam-dump.vcxproj | 52 +
build/MSVC/2010/schema-replace.vcxproj | 40 +
build/MSVC/2010/sff-dump.vcxproj | 43 +
build/MSVC/2010/sra-kar.vcxproj | 40 +
build/MSVC/2010/sra-pileup.vcxproj | 56 +
build/MSVC/2010/sra-stat.vcxproj | 40 +
build/MSVC/2010/sra-tools.sln | 336 +
build/MSVC/2010/srapath.vcxproj | 40 +
build/MSVC/2010/test-project.props | 15 +
build/MSVC/2010/test-sra.vcxproj | 41 +
build/MSVC/2010/vcf-loader.vcxproj | 35 +
build/MSVC/2010/vdb-common.props | 21 +
build/MSVC/2010/vdb-config.vcxproj | 46 +
build/MSVC/2010/vdb-copy.vcxproj | 51 +
build/MSVC/2010/vdb-decrypt.vcxproj | 41 +
build/MSVC/2010/vdb-dump.vcxproj | 53 +
build/MSVC/2010/vdb-encrypt.vcxproj | 41 +
build/MSVC/2010/vdb-lock.vcxproj | 40 +
build/MSVC/2010/vdb-passwd.vcxproj | 41 +
build/MSVC/2010/vdb-unlock.vcxproj | 39 +
build/MSVC/2010/vdb-validate.vcxproj | 40 +
build/Makefile.cc | 67 +
build/Makefile.clang | 11 +-
build/Makefile.env | 174 +-
build/Makefile.gcc | 4 +-
build/Makefile.install | 125 +
build/Makefile.linux | 17 +-
build/Makefile.mac | 6 +-
build/Makefile.rules | 5 +
build/Makefile.scm | 94 +
build/Makefile.shell | 48 +-
build/Makefile.sun | 96 +
build/Makefile.sun.cc | 155 +
build/Makefile.sun.gcc | 138 +
build/Makefile.targets | 22 +-
build/Makefile.vc++ | 13 +-
build/Makefile.win | 21 +-
.../asm-trace/asm-trace.xcodeproj/project.pbxproj | 4444 +++
build/Xcode/old-toolkit/.gitignore | 1 +
.../old-toolkit.xcodeproj/project.pbxproj | 2153 ++
build/cp.sh | 32 +
build/gprof2dot.py | 2763 ++
build/ld.linux.cmn.sh | 0
build/ld.linux.dlib.sh | 9 +-
build/ld.linux.exe.sh | 9 +-
build/{ld.mac.gcc.sh => ld.mac.clang.sh} | 0
build/ld.mac.cmn.sh | 0
build/ld.mac.dlib.sh | 4 +-
build/ld.mac.exe.sh | 11 +-
build/ld.rwin.dlib.sh | 363 +
build/ld.rwin.exe.sh | 366 +
build/ld.rwin.slib.sh | 123 +
build/ld.rwin.stub.sh | 59 +
build/ld.rwin.vc++.sh | 65 +
build/ld.sh | 35 +
build/ld.sun.cc.sh | 56 +
build/ld.sun.cmn.sh | 160 +
build/ld.sun.dlib.sh | 282 +
build/ld.sun.exe.sh | 299 +
build/ld.sun.ln.sh | 87 +
build/ld.sun.slib.sh | 135 +
build/ld.unix.cmn.sh | 0
build/ld.unix.slib.sh | 0
build/libexists.sh | 180 +
build/make-defs-xf.pl | 108 +
build/make-defs.pl | 247 +
build/run_remotely.sh | 124 +
build/scm-collect.sh | 42 +
build/scm.sh | 136 +
build/scm.txt | 117 +
build/sun-c++.sh | 100 +
build/sun-cc.sh | 93 +
build/tag-module.sh | 213 +
build/wait_for_file.sh | 65 +
build/win-cc.sh | 1 +
configuration-assistant.perl | 1228 -
configure | 45 +
debian/changelog | 11 +
debian/control | 7 +-
debian/copyright | 3 -
debian/patches/10_portability.patch | 11 +-
debian/patches/build-with-system-libbz2-libz.patch | 34 -
debian/patches/do_not_build_external_libs.patch | 14 -
debian/patches/hardening-format-security.patch | 43 -
debian/patches/hardening.patch | 31 +-
debian/patches/series | 3 -
debian/rules | 3 -
debian/watch | 3 +-
doc/help/html/abi-dump-help.html | 45 -
doc/help/html/abi-load-help.html | 41 -
doc/help/html/bam-load-help.html | 29 -
doc/help/html/copycat-help.html | 64 -
doc/help/html/crc32sum-help.html | 18 -
doc/help/html/fastq-dump-help.html | 88 -
doc/help/html/fastq-load-help.html | 41 -
doc/help/html/illumina-dump-help.html | 48 -
doc/help/html/illumina-load-help.html | 41 -
doc/help/html/kar-help.html | 66 -
doc/help/html/kdbmeta-help.html | 50 -
doc/help/html/kqsh-help.html | 19 -
doc/help/html/md5cp-help.html | 21 -
doc/help/html/rcexplain-help.html | 27 -
doc/help/html/sff-dump-help.html | 38 -
doc/help/html/sra-dump-help.html | 38 -
doc/help/html/sra-stat-help.html | 34 -
doc/help/html/srapath-help.html | 47 -
doc/help/html/srf-load-help.html | 41 -
doc/help/html/txt2kdb-help.html | 48 -
doc/help/html/vdb-dump-help.html | 45 -
doc/help/txt/abi-dump-help.txt | 19 -
doc/help/txt/abi-load-help.txt | 41 -
doc/help/txt/bam-loader-help.txt | 18 -
doc/help/txt/copycat-help.txt | 53 -
doc/help/txt/crc32sum-help.txt | 6 -
doc/help/txt/fastq-dump-help.txt | 57 -
doc/help/txt/fastq-load-help.txt | 41 -
doc/help/txt/illumina-dump-help.txt | 29 -
doc/help/txt/illumina-load-help.txt | 41 -
doc/help/txt/kar-help.txt | 48 -
doc/help/txt/kdbmeta-help.txt | 30 -
doc/help/txt/kqsh-help.txt | 7 -
doc/help/txt/md5cp-help.txt | 8 -
doc/help/txt/rcexplain-help.txt | 5 -
doc/help/txt/sff-dump-help.txt | 19 -
doc/help/txt/sra-dump-help.txt | 18 -
doc/help/txt/sra-stat-help.txt | 19 -
doc/help/txt/srapath-help.txt | 35 -
doc/help/txt/srf-load-help.txt | 41 -
doc/help/txt/txt2kdb-help.txt | 36 -
doc/help/txt/vdb-dump-help.txt | 34 -
interfaces/align/align-access.h | 342 -
interfaces/align/align.vschema | 1487 -
interfaces/align/alignsrc.h | 71 -
interfaces/align/bam.h | 831 -
interfaces/align/dna-reverse-cmpl.h | 43 -
interfaces/align/extern.h | 41 -
interfaces/align/iterator.h | 610 -
interfaces/align/manager.h | 69 -
interfaces/align/qstat.vschema | 87 -
interfaces/align/quality-quantizer.h | 49 -
interfaces/align/reader-refseq.h | 72 -
interfaces/align/reference.h | 150 -
interfaces/align/refseq-mgr.h | 86 -
interfaces/align/refseq.vschema | 100 -
interfaces/align/seq.vschema | 300 -
interfaces/align/writer-alignment.h | 177 -
interfaces/align/writer-cmn.h | 46 -
interfaces/align/writer-reference.h | 151 -
interfaces/align/writer-refseq.h | 89 -
interfaces/align/writer-sequence.h | 149 -
interfaces/cc/gcc/compiler.h | 39 -
interfaces/cc/gcc/i386/arch-impl.h | 400 -
interfaces/cc/gcc/i386/atomic.h | 162 -
interfaces/cc/gcc/i386/atomic32.h | 369 -
interfaces/cc/gcc/i386/bitstr.h | 39 -
interfaces/cc/gcc/i386/byteswap.h | 89 -
interfaces/cc/gcc/i386/strtol.h | 67 -
interfaces/cc/gcc/noarch/bitstr.h | 413 -
interfaces/cc/gcc/v128.h | 1088 -
interfaces/cc/gcc/va_copy.h | 49 -
interfaces/cc/gcc/x86_64/arch-impl.h | 361 -
interfaces/cc/gcc/x86_64/atomic.h | 176 -
interfaces/cc/gcc/x86_64/atomic32.h | 358 -
interfaces/cc/gcc/x86_64/atomic64.h | 358 -
interfaces/cc/gcc/x86_64/bitstr.h | 39 -
interfaces/cc/gcc/x86_64/byteswap.h | 89 -
interfaces/cc/gcc/x86_64/strtol.h | 69 -
interfaces/cc/icc/compiler.h | 39 -
interfaces/cc/vc++/compiler.h | 72 -
interfaces/cc/vc++/i386/arch-impl.h | 42 -
interfaces/cc/vc++/i386/bitstr.h | 39 -
interfaces/cc/vc++/noarch/arch-impl.h | 286 -
interfaces/cc/vc++/noarch/bitstr.h | 412 -
interfaces/cc/vc++/stdbool.h | 46 -
interfaces/cc/vc++/stdint.h | 50 -
interfaces/cc/vc++/va_copy.h | 43 -
interfaces/cc/vc++/x86_64/arch-impl.h | 42 -
interfaces/cc/vc++/x86_64/bitstr.h | 39 -
interfaces/ext/bzlib.h | 282 -
interfaces/ext/libxml/DOCBparser.h | 96 -
interfaces/ext/libxml/HTMLparser.h | 303 -
interfaces/ext/libxml/HTMLtree.h | 147 -
interfaces/ext/libxml/SAX.h | 173 -
interfaces/ext/libxml/SAX2.h | 176 -
interfaces/ext/libxml/c14n.h | 115 -
interfaces/ext/libxml/catalog.h | 182 -
interfaces/ext/libxml/chvalid.h | 230 -
interfaces/ext/libxml/debugXML.h | 217 -
interfaces/ext/libxml/dict.h | 69 -
interfaces/ext/libxml/encoding.h | 226 -
interfaces/ext/libxml/entities.h | 150 -
interfaces/ext/libxml/globals.h | 491 -
interfaces/ext/libxml/hash.h | 233 -
interfaces/ext/libxml/list.h | 137 -
interfaces/ext/libxml/nanoftp.h | 143 -
interfaces/ext/libxml/nanohttp.h | 81 -
interfaces/ext/libxml/parser.h | 1226 -
interfaces/ext/libxml/parserInternals.h | 611 -
interfaces/ext/libxml/pattern.h | 100 -
interfaces/ext/libxml/relaxng.h | 213 -
interfaces/ext/libxml/schemasInternals.h | 958 -
interfaces/ext/libxml/schematron.h | 142 -
interfaces/ext/libxml/threads.h | 84 -
interfaces/ext/libxml/tree.h | 1252 -
interfaces/ext/libxml/uri.h | 94 -
interfaces/ext/libxml/valid.h | 458 -
interfaces/ext/libxml/xinclude.h | 125 -
interfaces/ext/libxml/xlink.h | 189 -
interfaces/ext/libxml/xmlIO.h | 360 -
interfaces/ext/libxml/xmlautomata.h | 146 -
interfaces/ext/libxml/xmlerror.h | 944 -
interfaces/ext/libxml/xmlexports.h | 157 -
interfaces/ext/libxml/xmlmemory.h | 224 -
interfaces/ext/libxml/xmlmodule.h | 57 -
interfaces/ext/libxml/xmlreader.h | 424 -
interfaces/ext/libxml/xmlregexp.h | 222 -
interfaces/ext/libxml/xmlsave.h | 87 -
interfaces/ext/libxml/xmlschemas.h | 218 -
interfaces/ext/libxml/xmlschemastypes.h | 151 -
interfaces/ext/libxml/xmlstring.h | 140 -
interfaces/ext/libxml/xmlunicode.h | 202 -
interfaces/ext/libxml/xmlversion.h | 458 -
interfaces/ext/libxml/xmlwriter.h | 485 -
interfaces/ext/libxml/xpath.h | 546 -
interfaces/ext/libxml/xpathInternals.h | 630 -
interfaces/ext/libxml/xpointer.h | 114 -
interfaces/ext/magic.h | 89 -
interfaces/ext/regex.h | 557 -
interfaces/ext/zconf.h | 304 -
interfaces/ext/zlib.h | 1613 -
interfaces/insdc/insdc.h | 277 -
interfaces/insdc/insdc.vschema | 210 -
interfaces/insdc/seq.vschema | 210 -
interfaces/insdc/sra.h | 110 -
interfaces/insdc/sra.vschema | 484 -
interfaces/kapp/args.h | 339 -
interfaces/kapp/extern.h | 47 -
interfaces/kapp/loader-file.h | 122 -
interfaces/kapp/loader-meta.h | 51 -
interfaces/kapp/log-xml.h | 76 -
interfaces/kapp/main.h | 167 -
interfaces/kapp/progressbar.h | 82 -
interfaces/kapp/queue-file.h | 149 -
interfaces/kdb/btree.h | 371 -
interfaces/kdb/column.h | 302 -
interfaces/kdb/consistency-check.h | 142 -
interfaces/kdb/database.h | 270 -
interfaces/kdb/extern.h | 41 -
interfaces/kdb/index.h | 309 -
interfaces/kdb/kdb-priv.h | 156 -
interfaces/kdb/manager.h | 182 -
interfaces/kdb/meta.h | 411 -
interfaces/kdb/meta.hpp | 487 -
interfaces/kdb/namelist.h | 81 -
interfaces/kdb/table.h | 274 -
interfaces/kfc/callconv.h | 53 -
interfaces/kfc/ctx.h | 214 -
interfaces/kfc/defs.h | 159 -
interfaces/kfc/except.h | 149 -
interfaces/kfc/extern.h | 68 -
interfaces/kfc/rc.h | 352 -
interfaces/kfc/rsrc.h | 80 -
interfaces/kfc/xc.h | 94 -
interfaces/kfc/xcdefs.h | 81 -
interfaces/kfc/xcext.h | 64 -
interfaces/kfc/xcgen.h | 68 -
interfaces/kfg/config.h | 407 -
interfaces/kfg/extern.h | 41 -
interfaces/kfg/kart.h | 90 -
interfaces/kfg/keystore-priv.h | 92 -
interfaces/kfg/keystore.h | 153 -
interfaces/kfg/kfg-priv.h | 90 -
interfaces/kfg/repository.h | 290 -
interfaces/kfs/arc.h | 142 -
interfaces/kfs/arrayfile.h | 180 -
interfaces/kfs/buffile.h | 94 -
interfaces/kfs/bzip.h | 77 -
interfaces/kfs/cacheteefile.h | 147 -
interfaces/kfs/countfile.h | 73 -
interfaces/kfs/crc.h | 292 -
interfaces/kfs/defs.h | 115 -
interfaces/kfs/directory.h | 522 -
interfaces/kfs/directory.hpp | 582 -
interfaces/kfs/dyload.h | 223 -
interfaces/kfs/extern.h | 41 -
interfaces/kfs/ffext.h | 48 -
interfaces/kfs/ffmagic.h | 49 -
interfaces/kfs/file.h | 287 -
interfaces/kfs/file.hpp | 147 -
interfaces/kfs/fileformat.h | 140 -
interfaces/kfs/gzip.h | 77 -
interfaces/kfs/impl.h | 337 -
interfaces/kfs/kfs-priv.h | 95 -
interfaces/kfs/lockfile.h | 116 -
interfaces/kfs/md5.h | 289 -
interfaces/kfs/mmap.h | 134 -
interfaces/kfs/nullfile.h | 62 -
interfaces/kfs/pagefile.h | 191 -
interfaces/kfs/pmem.h | 157 -
interfaces/kfs/quickmount.h | 61 -
interfaces/kfs/ramfile.h | 75 -
interfaces/kfs/readheadfile.h | 86 -
interfaces/kfs/sra.h | 191 -
interfaces/kfs/subfile.h | 64 -
interfaces/kfs/tar.h | 94 -
interfaces/kfs/teefile.h | 66 -
interfaces/kfs/toc.h | 148 -
interfaces/klib/callconv.h | 34 -
interfaces/klib/checksum.h | 152 -
interfaces/klib/container.h | 455 -
interfaces/klib/data-buffer.h | 206 -
interfaces/klib/debug.h | 541 -
interfaces/klib/defs.h | 118 -
interfaces/klib/extern.h | 51 -
interfaces/klib/impl.h | 96 -
interfaces/klib/klib-priv.h | 106 -
interfaces/klib/ksort-macro.h | 257 -
interfaces/klib/log.h | 380 -
interfaces/klib/logfmt.h | 62 -
interfaces/klib/misc.h | 48 -
interfaces/klib/namelist.h | 181 -
interfaces/klib/namelist.hpp | 130 -
interfaces/klib/out.h | 86 -
interfaces/klib/pack.h | 138 -
interfaces/klib/pbstree.h | 287 -
interfaces/klib/printf.h | 406 -
interfaces/klib/ptrie.h | 296 -
interfaces/klib/rc.h | 185 -
interfaces/klib/refcount.h | 264 -
interfaces/klib/report.h | 103 -
interfaces/klib/sort.h | 123 -
interfaces/klib/sra-release-version.h | 99 -
interfaces/klib/status.h | 133 -
interfaces/klib/symbol.h | 146 -
interfaces/klib/symtab.h | 225 -
interfaces/klib/text.h | 498 -
interfaces/klib/time.h | 96 -
interfaces/klib/token.h | 254 -
interfaces/klib/trie.h | 293 -
interfaces/klib/vector.h | 428 -
interfaces/klib/vlen-encode.h | 161 -
interfaces/klib/writer.h | 170 -
interfaces/kns/adapt.h | 89 -
interfaces/kns/ascp.h | 99 -
interfaces/kns/endpoint.h | 121 -
interfaces/kns/extern.h | 41 -
interfaces/kns/http.h | 301 -
interfaces/kns/impl.h | 111 -
interfaces/kns/manager-ext.h | 59 -
interfaces/kns/manager.h | 96 -
interfaces/kns/socket.h | 122 -
interfaces/kns/stream.h | 210 -
interfaces/kproc/barrier.h | 75 -
interfaces/kproc/barrier.hpp | 79 -
interfaces/kproc/cond.h | 103 -
interfaces/kproc/cond.hpp | 107 -
interfaces/kproc/extern.h | 41 -
interfaces/kproc/impl.h | 104 -
interfaces/kproc/lock.h | 144 -
interfaces/kproc/lock.hpp | 163 -
interfaces/kproc/procmgr.h | 115 -
interfaces/kproc/q-extern.h | 41 -
interfaces/kproc/queue.h | 116 -
interfaces/kproc/sem.h | 138 -
interfaces/kproc/sem.hpp | 134 -
interfaces/kproc/task.h | 83 -
interfaces/kproc/thread.h | 91 -
interfaces/kproc/thread.hpp | 98 -
interfaces/kproc/timeout.h | 64 -
interfaces/krypto/cipher-impl.h | 1 -
interfaces/krypto/cipher-priv.h | 1 -
interfaces/krypto/cipher-test.h | 49 -
interfaces/krypto/cipher.h | 208 -
interfaces/krypto/ciphermgr-priv.h | 38 -
interfaces/krypto/ciphermgr.h | 98 -
interfaces/krypto/encfile-priv.h | 250 -
interfaces/krypto/encfile.h | 134 -
interfaces/krypto/extern.h | 48 -
interfaces/krypto/key.h | 103 -
interfaces/krypto/manager-priv.h | 26 -
interfaces/krypto/manager.h | 33 -
interfaces/krypto/reencfile.h | 91 -
interfaces/krypto/rng-impl.h | 86 -
interfaces/krypto/rng.h | 68 -
interfaces/krypto/testciphermgr.h | 58 -
interfaces/krypto/wgaencrypt.h | 128 -
interfaces/ktst/test_tools.hpp | 22 -
interfaces/ktst/unit_test.hpp | 255 -
interfaces/ktst/unit_test_suite.hpp | 491 -
interfaces/kxml/xml.h | 382 -
interfaces/loader/alignment-writer.h | 109 -
interfaces/loader/common-reader-priv.h | 300 -
interfaces/loader/common-reader.h | 486 -
interfaces/loader/common-writer.h | 192 -
interfaces/loader/mmarray.h | 50 -
interfaces/loader/reference-writer.h | 78 -
interfaces/loader/sequence-writer.h | 91 -
interfaces/ncbi/clip.vschema | 143 -
interfaces/ncbi/extern.h | 41 -
interfaces/ncbi/ncbi.vschema | 195 -
interfaces/ncbi/seq.vschema | 889 -
interfaces/ncbi/spotname.vschema | 377 -
interfaces/ncbi/sra.vschema | 743 -
interfaces/ncbi/stats.vschema | 119 -
interfaces/ncbi/vdb-blast-priv.h | 51 -
interfaces/ncbi/vdb-blast.h | 489 -
interfaces/ncbi/wgs-contig.h | 183 -
interfaces/ncbi/wgs-contig.vschema | 695 -
interfaces/os/linux/os-native.h | 43 -
interfaces/os/mac/byteswap.h | 39 -
interfaces/os/mac/endian.h | 39 -
interfaces/os/mac/os-native.h | 114 -
interfaces/os/unix/sysalloc.h | 40 -
interfaces/os/unix/unix-native.h | 58 -
interfaces/os/win/atomic.h | 143 -
interfaces/os/win/atomic32.h | 193 -
interfaces/os/win/atomic64.h | 193 -
interfaces/os/win/byteswap.h | 44 -
interfaces/os/win/endian.h | 42 -
interfaces/os/win/os-native.h | 207 -
interfaces/os/win/strtol.h | 149 -
interfaces/os/win/sysalloc.h | 69 -
interfaces/search/extern.h | 41 -
interfaces/search/grep.h | 263 -
interfaces/search/nucstrstr.h | 153 -
interfaces/sra/454.vschema | 289 -
interfaces/sra/abi.h | 167 -
interfaces/sra/abi.vschema | 241 -
interfaces/sra/extern.h | 41 -
interfaces/sra/fastq.h | 191 -
interfaces/sra/helicos.vschema | 85 -
interfaces/sra/illumina.h | 170 -
interfaces/sra/illumina.vschema | 403 -
interfaces/sra/impl.h | 121 -
interfaces/sra/ion-torrent.vschema | 117 -
interfaces/sra/pacbio.h | 66 -
interfaces/sra/path-extern.h | 41 -
interfaces/sra/pevents.vschema | 91 -
interfaces/sra/rd-extern.h | 41 -
interfaces/sra/sch-extern.h | 41 -
interfaces/sra/sff-file.h | 110 -
interfaces/sra/sff.h | 147 -
interfaces/sra/sradb-priv.h | 407 -
interfaces/sra/sradb.h | 545 -
interfaces/sra/sradb.hpp | 441 -
interfaces/sra/srapath.h | 181 -
interfaces/sra/srapath.hpp | 176 -
interfaces/sra/sraschema.h | 72 -
interfaces/sra/types.h | 350 -
interfaces/sra/wsradb.h | 242 -
interfaces/sra/wsradb.hpp | 591 -
interfaces/vdb/blob.h | 147 -
interfaces/vdb/built-in.vschema | 397 -
interfaces/vdb/cursor.h | 441 -
interfaces/vdb/cursor.hpp | 388 -
interfaces/vdb/database.h | 334 -
interfaces/vdb/dependencies.h | 231 -
interfaces/vdb/extern.h | 47 -
interfaces/vdb/manager.h | 200 -
interfaces/vdb/manager.hpp | 371 -
interfaces/vdb/report.h | 92 -
interfaces/vdb/schema.h | 460 -
interfaces/vdb/table.h | 401 -
interfaces/vdb/table.hpp | 328 -
interfaces/vdb/types.h | 39 -
interfaces/vdb/types.hpp | 230 -
interfaces/vdb/vdb-priv.h | 319 -
interfaces/vdb/vdb.vschema | 820 -
interfaces/vdb/xform.h | 824 -
interfaces/vfs/extern.h | 47 -
interfaces/vfs/manager-priv.h | 126 -
interfaces/vfs/manager.h | 319 -
interfaces/vfs/path-priv.h | 266 -
interfaces/vfs/path.h | 253 -
interfaces/vfs/resolver.h | 263 -
konfigure.perl | 1204 +
libs/Makefile | 75 -
libs/align/Makefile | 151 -
libs/align/al_iterator.c | 562 -
libs/align/align-access.c | 792 -
libs/align/align_mgr.c | 108 -
libs/align/bam-priv.h | 48 -
libs/align/bam.c | 4906 ---
libs/align/debug.h | 77 -
libs/align/dna-reverse-cmpl.c | 80 -
libs/align/pl_iterator.c | 686 -
libs/align/quality-quantizer.c | 105 -
libs/align/reader-cmn.c | 317 -
libs/align/reader-cmn.h | 81 -
libs/align/reader-refseq.c | 255 -
libs/align/ref_iterator.c | 866 -
libs/align/reference-cmn.c | 43 -
libs/align/reference-cmn.h | 38 -
libs/align/reference.c | 1947 --
libs/align/refseq-mgr-priv.h | 35 -
libs/align/refseq-mgr.c | 813 -
libs/align/writer-alignment.c | 430 -
libs/align/writer-cmn.c | 568 -
libs/align/writer-priv.h | 151 -
libs/align/writer-ref.c | 481 -
libs/align/writer-ref.h | 106 -
libs/align/writer-reference.c | 2584 --
libs/align/writer-refseq.c | 179 -
libs/align/writer-sequence.c | 636 -
libs/ascp/Makefile | 80 -
libs/ascp/ascp-priv.h | 74 -
libs/ascp/ascp.c | 745 -
libs/ascp/linux/ascp-path.c | 89 -
libs/ascp/mac/ascp-path.c | 65 -
libs/ascp/unix/connect.c | 555 -
libs/ascp/win/ascp-path.c | 26 -
libs/ascp/win/connect.c | 510 -
libs/axf/Makefile | 133 -
libs/axf/align-local_ref_id.c | 130 -
libs/axf/align-local_ref_start.c | 131 -
libs/axf/align-ref-name.c | 158 -
libs/axf/align-ref-pos.c | 246 -
libs/axf/align-ref-seq-id.c | 157 -
libs/axf/align-restore-read.c | 139 -
libs/axf/cigar.c | 1914 --
libs/axf/generate-mismatch-qual.c | 148 -
libs/axf/get-sam-flags.c | 206 -
libs/axf/get_mate_align_ids.c | 271 -
libs/axf/make-cmp-read_desc.c | 156 -
libs/axf/mismatch-restore-qual.c | 129 -
libs/axf/not-my-row.c | 72 -
libs/axf/project_read_from_sequence.c | 228 -
libs/axf/raw-restore-qual.c | 91 -
libs/axf/raw-restore-read.c | 114 -
libs/axf/ref-preserve_qual.c | 363 -
libs/axf/ref-restore-read.c | 162 -
libs/axf/ref-tbl-sub-select.c | 429 -
libs/axf/ref-tbl.c | 85 -
libs/axf/ref-tbl.h | 32 -
libs/axf/refseq-stats.c | 148 -
libs/axf/seq-construct-read.c | 125 -
libs/axf/seq-restore-read.c | 216 -
libs/axf/template-len.c | 127 -
libs/blast/Makefile | 85 -
libs/blast/blast.c | 5243 ---
libs/kapp/Makefile | 115 -
libs/kapp/args.c | 2004 --
libs/kapp/args_debug.h | 47 -
libs/kapp/loader-file.c | 643 -
libs/kapp/loader-meta.c | 98 -
libs/kapp/log-xml.c | 416 -
libs/kapp/main-priv.h | 71 -
libs/kapp/main.c | 431 -
libs/kapp/progressbar.c | 199 -
libs/kapp/queue-file.c | 925 -
libs/kapp/tokenizer.c | 525 -
libs/kapp/unix/sysmain.c | 238 -
libs/kapp/win/sysmain.c | 272 -
libs/kdb/Makefile | 153 -
libs/kdb/btree.c | 3055 --
libs/kdb/cc-priv.h | 51 -
libs/kdb/coldata-priv.h | 126 -
libs/kdb/coldata.c | 188 -
libs/kdb/colfmt-priv.h | 339 -
libs/kdb/colidx-priv.h | 117 -
libs/kdb/colidx.c | 184 -
libs/kdb/colidx0-priv.h | 88 -
libs/kdb/colidx0.c | 368 -
libs/kdb/colidx1-priv.h | 110 -
libs/kdb/colidx1.c | 423 -
libs/kdb/colidx2-priv.h | 99 -
libs/kdb/colidx2.c | 279 -
libs/kdb/column-cc.c | 224 -
libs/kdb/column-priv.h | 94 -
libs/kdb/column.c | 876 -
libs/kdb/database-cc.c | 338 -
libs/kdb/database-cmn.c | 495 -
libs/kdb/database-priv.h | 112 -
libs/kdb/database.c | 706 -
libs/kdb/dbcc-cmn.c | 141 -
libs/kdb/dbmgr-cmn.c | 485 -
libs/kdb/dbmgr-priv.h | 128 -
libs/kdb/dbmgr.c | 420 -
libs/kdb/idstats-priv.h | 74 -
libs/kdb/idstats.c | 269 -
libs/kdb/idxblk-priv.h | 136 -
libs/kdb/idxblk.c | 695 -
libs/kdb/index-cmn.h | 286 -
libs/kdb/index-priv.h | 134 -
libs/kdb/index.c | 1006 -
libs/kdb/kdb-priv.h | 122 -
libs/kdb/kdb.c | 938 -
libs/kdb/kdbfmt-priv.h | 76 -
libs/kdb/libkdb.vers.h | 27 -
libs/kdb/libwkdb.vers.h | 27 -
libs/kdb/meta.c | 2141 --
libs/kdb/ptrieval-v1.c | 265 -
libs/kdb/ptrieval-v2.c | 396 -
libs/kdb/table-cc.c | 378 -
libs/kdb/table-priv.h | 81 -
libs/kdb/table.c | 706 -
libs/kdb/trieidx-priv.h | 74 -
libs/kdb/trieidx-v1.c | 222 -
libs/kdb/trieidx-v2.c | 1047 -
libs/kdb/trieval-v1.c | 49 -
libs/kdb/trieval-v2.c | 49 -
libs/kdb/u64idx-v3.c | 162 -
libs/kdb/wcoldata-priv.h | 172 -
libs/kdb/wcoldata.c | 342 -
libs/kdb/wcolidx-priv.h | 161 -
libs/kdb/wcolidx.c | 634 -
libs/kdb/wcolidx0-priv.h | 148 -
libs/kdb/wcolidx0.c | 747 -
libs/kdb/wcolidx1-priv.h | 147 -
libs/kdb/wcolidx1.c | 857 -
libs/kdb/wcolidx2-priv.h | 114 -
libs/kdb/wcolidx2.c | 241 -
libs/kdb/wcolumn-priv.h | 120 -
libs/kdb/wcolumn.c | 2437 --
libs/kdb/wdatabase-priv.h | 95 -
libs/kdb/wdatabase.c | 1503 -
libs/kdb/wdbmgr.c | 349 -
libs/kdb/werror-priv.h | 59 -
libs/kdb/widxblk-priv.h | 195 -
libs/kdb/widxblk.c | 546 -
libs/kdb/windex-priv.h | 230 -
libs/kdb/windex.c | 1889 --
libs/kdb/wkdb-priv.h | 160 -
libs/kdb/wkdb.c | 1417 -
libs/kdb/wmeta.c | 3526 ---
libs/kdb/wtable-priv.h | 106 -
libs/kdb/wtable.c | 1590 -
libs/kdb/wtrieidx-v1.c | 1100 -
libs/kdb/wtrieidx-v2.c | 2560 --
libs/kdb/wu64idx-v3.c | 416 -
libs/kfg/Makefile | 99 -
libs/kfg/config-grammar.c | 1724 -
libs/kfg/config-lex.c | 2511 --
libs/kfg/config-tokens.h | 75 -
libs/kfg/config.c | 3592 ---
libs/kfg/default.kfg | 56 -
libs/kfg/kart.c | 715 -
libs/kfg/keystore.c | 836 -
libs/kfg/kfg-parse.h | 81 -
libs/kfg/report-kfg.c | 506 -
libs/kfg/repository.c | 1190 -
libs/kfs/Makefile | 179 -
libs/kfs/arc.c | 4019 ---
libs/kfs/arrayfile.c | 423 -
libs/kfs/buffile-read.c | 265 -
libs/kfs/buffile-write.c | 368 -
libs/kfs/buffile.c | 573 -
libs/kfs/bzip.c | 838 -
libs/kfs/cacheteefile.c | 1689 -
libs/kfs/countfile.c | 652 -
libs/kfs/crc32.c | 1771 --
libs/kfs/dir_test.c | 54 -
libs/kfs/directory.c | 1538 -
libs/kfs/ffext.c | 805 -
libs/kfs/ffkey.c | 833 -
libs/kfs/ffmagic.c | 942 -
libs/kfs/file.c | 865 -
libs/kfs/fileformat-priv.h | 124 -
libs/kfs/fileformat.c | 290 -
libs/kfs/from_to_namelist.c | 307 -
libs/kfs/gzip.c | 646 -
libs/kfs/impl.h | 120 -
libs/kfs/karc-priv.h | 43 -
libs/kfs/kfs-priv.h | 47 -
libs/kfs/lockfile.c | 350 -
libs/kfs/md5.c | 1901 --
libs/kfs/mmap-priv.h | 107 -
libs/kfs/mmap.c | 754 -
libs/kfs/nullfile.c | 273 -
libs/kfs/pagefile.c | 1283 -
libs/kfs/pmem.c | 1047 -
libs/kfs/quickmount.c | 967 -
libs/kfs/ramfile.c | 424 -
libs/kfs/readheadfile.c | 294 -
libs/kfs/report.c | 169 -
libs/kfs/sra.c | 486 -
libs/kfs/subfile.c | 337 -
libs/kfs/tar.c | 2639 --
libs/kfs/teefile.c | 532 -
libs/kfs/toc-priv.h | 841 -
libs/kfs/toc.c | 1738 -
libs/kfs/tocdir.c | 411 -
libs/kfs/tocentry.c | 1748 -
libs/kfs/tocfile.c | 636 -
libs/kfs/unix/sysdir-priv.h | 68 -
libs/kfs/unix/sysdir.c | 2408 --
libs/kfs/unix/sysdll.c | 1422 -
libs/kfs/unix/sysfile-priv.h | 75 -
libs/kfs/unix/sysfile.c | 1057 -
libs/kfs/unix/syslockfile.c | 215 -
libs/kfs/unix/sysmmap-priv.h | 68 -
libs/kfs/unix/sysmmap.c | 143 -
libs/kfs/win/lnk_tools.c | 518 -
libs/kfs/win/sysdir-priv.h | 92 -
libs/kfs/win/sysdir.c | 2955 --
libs/kfs/win/sysdll.c | 1410 -
libs/kfs/win/sysfile-priv.h | 68 -
libs/kfs/win/sysfile.c | 1023 -
libs/kfs/win/syslockfile.c | 67 -
libs/kfs/win/sysmmap-priv.h | 71 -
libs/kfs/win/sysmmap.c | 138 -
libs/klib/Judy.h | 629 -
libs/klib/Makefile | 142 -
libs/klib/SHA-32bit.c | 307 -
libs/klib/SHA-64bit.c | 270 -
libs/klib/bsearch.c | 77 -
libs/klib/bstpersist.c | 252 -
libs/klib/container.c | 1646 -
libs/klib/cp1252.c | 65 -
libs/klib/crc32.c | 89 -
libs/klib/data-buffer.c | 501 -
libs/klib/debug.c | 311 -
libs/klib/iso8859-1.c | 42 -
libs/klib/iso8859.c | 205 -
libs/klib/judy-vector.c | 892 -
libs/klib/judy/Judy1.h | 549 -
libs/klib/judy/JudyByCount.c | 952 -
libs/klib/judy/JudyByCountWithDefs.c | 4 -
libs/klib/judy/JudyCascade.c | 1940 --
libs/klib/judy/JudyCount.c | 1193 -
libs/klib/judy/JudyCreateBranch.c | 312 -
libs/klib/judy/JudyDecascade.c | 1204 -
libs/klib/judy/JudyDel.c | 2144 --
libs/klib/judy/JudyFirst.c | 211 -
libs/klib/judy/JudyFreeArray.c | 361 -
libs/klib/judy/JudyGet.c | 1092 -
libs/klib/judy/JudyHS.c | 770 -
libs/klib/judy/JudyHS.h | 35 -
libs/klib/judy/JudyIns.c | 1871 --
libs/klib/judy/JudyInsArray.c | 1176 -
libs/klib/judy/JudyInsertBranch.c | 133 -
libs/klib/judy/JudyL.h | 503 -
libs/klib/judy/JudyMalloc.c | 86 -
libs/klib/judy/JudyMallocIF.c | 780 -
libs/klib/judy/JudyMemActive.c | 257 -
libs/klib/judy/JudyMemUsed.c | 59 -
libs/klib/judy/JudyNext.c | 2 -
libs/klib/judy/JudyNextEmpty.c | 2 -
libs/klib/judy/JudyPrev.c | 2 -
libs/klib/judy/JudyPrevEmpty.c | 2 -
libs/klib/judy/JudyPrevNext.c | 1888 --
libs/klib/judy/JudyPrevNextEmpty.c | 1388 -
libs/klib/judy/JudyPrintJP.c | 399 -
libs/klib/judy/JudyPrivate.h | 1610 -
libs/klib/judy/JudyPrivate1L.h | 483 -
libs/klib/judy/JudyPrivateBranch.h | 777 -
libs/klib/judy/JudySL.c | 1125 -
libs/klib/judy/JudyTablesGen.c | 294 -
libs/klib/judy/Makefile | 190 -
libs/klib/judy/j__udyGet.c | 2 -
libs/klib/ksort.c | 97 -
libs/klib/log-priv.h | 96 -
libs/klib/log.c | 984 -
libs/klib/maybeswap.h | 57 -
libs/klib/md5.c | 421 -
libs/klib/namelist.c | 149 -
libs/klib/out.c | 126 -
libs/klib/pack.c | 517 -
libs/klib/pbstree-impl.c | 847 -
libs/klib/pbstree-native.c | 30 -
libs/klib/pbstree-priv.h | 664 -
libs/klib/pbstree-swapped.c | 30 -
libs/klib/pbstree.c | 395 -
libs/klib/printf.c | 3541 ---
libs/klib/ptpersist.c | 1099 -
libs/klib/ptrie.c | 1956 --
libs/klib/qsort.c | 311 -
libs/klib/rc-idx-tbl.c | 39 -
libs/klib/rc-tbl.c | 36 -
libs/klib/refcount.c | 499 -
libs/klib/release-vers.h | 41 -
libs/klib/report.c | 854 -
libs/klib/sra-release-version.c | 328 -
libs/klib/status-rc-strings.c | 39 -
libs/klib/status-rc.c | 156 -
libs/klib/status.c | 436 -
libs/klib/symtab.c | 736 -
libs/klib/text.c | 841 -
libs/klib/token.c | 1290 -
libs/klib/trie-priv.h | 237 -
libs/klib/trie.c | 1486 -
libs/klib/trieval.c | 168 -
libs/klib/unix/misc.c | 33 -
libs/klib/unix/syserrcode.c | 46 -
libs/klib/unix/syslog.c | 209 -
libs/klib/unix/systime.c | 139 -
libs/klib/unix/syswriter.c | 159 -
libs/klib/unpack.c | 833 -
libs/klib/utf8.c | 836 -
libs/klib/vector.c | 626 -
libs/klib/vector_namelist.c | 357 -
libs/klib/vlen-encode.c | 773 -
libs/klib/win/misc.c | 33 -
libs/klib/win/sysalloc.c | 68 -
libs/klib/win/syserrcode.c | 85 -
libs/klib/win/syslog.c | 120 -
libs/klib/win/systime.c | 278 -
libs/klib/win/syswriter.c | 179 -
libs/klib/writer-priv.h | 169 -
libs/klib/writer.c | 634 -
libs/kns/Makefile | 132 -
libs/kns/endpoint.c | 109 -
libs/kns/http-priv.h | 116 -
libs/kns/http-test.c | 368 -
libs/kns/http.c | 3158 --
libs/kns/kns_manager-ext.c | 157 -
libs/kns/kns_manager.c | 345 -
libs/kns/linux/sysendpoint.c | 158 -
libs/kns/linux/syspoll.c | 107 -
libs/kns/mac/sysendpoint.c | 140 -
libs/kns/mac/syspoll.c | 96 -
libs/kns/manager.c | 307 -
libs/kns/mgr-priv.h | 57 -
libs/kns/poll-priv.h | 51 -
libs/kns/stream-from-files.c | 168 -
libs/kns/stream-from-streams.c | 150 -
libs/kns/stream-priv.h | 40 -
libs/kns/stream.c | 780 -
libs/kns/sysmgr.h | 41 -
libs/kns/undyinghttp.c | 362 -
libs/kns/unix/sysmgr.c | 37 -
libs/kns/unix/syssock.c | 875 -
libs/kns/unix/sysstream.c | 251 -
libs/kns/url-fetcher-curl.c | 255 -
libs/kns/url-fetcher-impl.h | 109 -
libs/kns/url-fetcher.c | 129 -
libs/kns/win/sysendpoint.c | 148 -
libs/kns/win/sysmgr.c | 65 -
libs/kns/win/syssock.c | 1296 -
libs/kns/win/sysstream.c | 232 -
libs/kproc/Makefile | 153 -
libs/kproc/bsd/syslock-priv.h | 72 -
libs/kproc/bsd/syslock.c | 932 -
libs/kproc/linux/sysbarrier.c | 170 -
libs/kproc/linux/syslock-priv.h | 68 -
libs/kproc/linux/syslock.c | 617 -
libs/kproc/procmgr.c | 412 -
libs/kproc/queue.c | 398 -
libs/kproc/sem.c | 435 -
libs/kproc/stbarrier.c | 128 -
libs/kproc/stcond.c | 152 -
libs/kproc/stlock.c | 311 -
libs/kproc/stsem.c | 233 -
libs/kproc/stthread.c | 149 -
libs/kproc/sttimeout.c | 65 -
libs/kproc/task.c | 156 -
libs/kproc/unix/syscond-priv.h | 78 -
libs/kproc/unix/syscond.c | 320 -
libs/kproc/unix/systhread.c | 272 -
libs/kproc/unix/systimeout.c | 86 -
libs/kproc/win/syscond-priv.h | 79 -
libs/kproc/win/syscond.c | 500 -
libs/kproc/win/syslock-priv.h | 67 -
libs/kproc/win/syslock.c | 725 -
libs/krypto/Makefile | 292 -
libs/krypto/aes-byte.c | 236 -
libs/krypto/aes-ncbi-priv.h | 227 -
libs/krypto/aes-ncbi.c | 2644 --
libs/krypto/aes-priv.h | 94 -
libs/krypto/aes.c | 1 -
libs/krypto/aes_core.c | 1181 -
libs/krypto/blockcipher-impl.h | 187 -
libs/krypto/blockcipher-priv.h | 90 -
libs/krypto/blockcipher.c | 3 -
libs/krypto/cipher-byte.c | 522 -
libs/krypto/cipher-impl.h | 174 -
libs/krypto/cipher-no-vec.c | 41 -
libs/krypto/cipher-priv.h | 79 -
libs/krypto/cipher-vec.c | 808 -
libs/krypto/cipher.c | 538 -
libs/krypto/ciphermgr.c | 295 -
libs/krypto/compile-test.c | 50 -
libs/krypto/csprng.c | 163 -
libs/krypto/encfile-priv.h | 163 -
libs/krypto/encfile.c | 2122 --
libs/krypto/encfilev2.c | 2589 --
libs/krypto/key.c | 126 -
libs/krypto/manager.c | 11 -
libs/krypto/ncbi-priv.h | 122 -
libs/krypto/no-null-ncbi.c | 59 -
libs/krypto/null-ncbi-priv.h | 56 -
libs/krypto/null-ncbi.c | 251 -
libs/krypto/reencfile.c | 1255 -
libs/krypto/rng-impl.h | 91 -
libs/krypto/rng-priv.h | 0
libs/krypto/rng.c | 120 -
libs/krypto/testcipher.c | 76 -
libs/krypto/wgaencrypt.c | 1254 -
libs/ktst/Makefile | 81 -
libs/ktst/testcase.cpp | 95 -
libs/ktst/testenv.cpp | 514 -
libs/ktst/testrunner.cpp | 77 -
libs/ktst/unix/runprocesstestcase.cpp | 131 -
libs/ktst/win/runprocesstestcase.cpp | 161 -
libs/kxml/Makefile | 124 -
libs/kxml/xml.c | 1705 -
libs/kxml/xtoc-parsexml.c | 576 -
libs/kxml/xtoc-priv.h | 124 -
libs/kxml/xtoc.c | 3464 --
libs/loader/Makefile | 87 -
libs/loader/alignment-writer.c | 262 -
libs/loader/common-reader.c | 614 -
libs/loader/common-writer.c | 2074 --
libs/loader/mmarray.c | 131 -
libs/loader/reference-writer.c | 462 -
libs/loader/sequence-writer.c | 361 -
libs/ncbi-vdb/Makefile | 152 -
libs/ncbi-vdb/libncbi-vdb.vers | 1 -
libs/ncbi-vdb/libncbi-wvdb.vers | 1 -
libs/search/Makefile | 97 -
libs/search/agrep-dp.c | 881 -
libs/search/agrep-myers.c | 586 -
libs/search/agrep-myersunltd.c | 1039 -
libs/search/agrep-wumanber.c | 415 -
libs/search/debug.h | 43 -
libs/search/fgrep-aho.c | 348 -
libs/search/fgrep-boyermoore.c | 458 -
libs/search/fgrep-dumb.c | 326 -
libs/search/nucstrstr-icc-i386-dbg.pic.s | 31488 -------------------
libs/search/nucstrstr-icc-i386-prof.pic.s | 7600 -----
libs/search/nucstrstr-icc-i386-rel.pic.s | 6711 ----
libs/search/nucstrstr-icc-x86_64-dbg.pic.s | 25447 ---------------
libs/search/nucstrstr-icc-x86_64-prof.pic.s | 13651 --------
libs/search/nucstrstr-icc-x86_64-rel.pic.s | 9908 ------
libs/search/nucstrstr.c | 5313 ----
libs/search/search-priv.h | 137 -
libs/search/search.c | 285 -
libs/sra/Makefile | 234 -
libs/sra/built-in.vschema | 580 -
libs/sra/libsradb.vers.h | 27 -
libs/sra/reader-abi.c | 473 -
libs/sra/reader-cmn.c | 379 -
libs/sra/reader-cmn.h | 161 -
libs/sra/reader-fastq.c | 622 -
libs/sra/reader-illumina.c | 565 -
libs/sra/reader-sff.c | 380 -
libs/sra/sra-debug.h | 42 -
libs/sra/sra-dflt-schema.c | 550 -
libs/sra/sra-priv.h | 183 -
libs/sra/sra-schema.c | 4095 ---
libs/sra/sracache.c | 559 -
libs/sra/sracol.c | 235 -
libs/sra/sramgr-cmn.c | 572 -
libs/sra/sramgr.c | 186 -
libs/sra/sraschema-priv.h | 36 -
libs/sra/sraschema-stub.c | 51 -
libs/sra/sraschema.c | 74 -
libs/sra/sratbl-cmn.c | 1397 -
libs/sra/sratbl.c | 118 -
libs/sra/types.c | 298 -
libs/sra/wsramgr.c | 165 -
libs/sra/wsraschema-stub.c | 51 -
libs/sra/wsratbl.c | 649 -
libs/sraxf/Makefile | 143 -
libs/sraxf/bio-start.c | 95 -
libs/sraxf/color-from-dna.c | 151 -
libs/sraxf/denormalize.c | 231 -
libs/sraxf/dna-from-color.c | 150 -
libs/sraxf/dynamic-454-read-descriptor.c | 303 -
libs/sraxf/extract-coordinates.c | 353 -
libs/sraxf/extract-name_coord.c | 242 -
libs/sraxf/extract-name_fmt.c | 240 -
libs/sraxf/extract-spot_name.c | 105 -
libs/sraxf/fix_read_seg_impl.h | 169 -
libs/sraxf/format-spot-name.c | 332 -
libs/sraxf/fpcodec.c | 267 -
libs/sraxf/index_lookup.c | 269 -
libs/sraxf/make-position.c | 133 -
libs/sraxf/name-tokenizer.h | 121 -
libs/sraxf/normalize.c | 240 -
libs/sraxf/prefix-tree-to-name.c | 162 -
libs/sraxf/process-position.c | 198 -
libs/sraxf/qual4_codec.h | 43 -
libs/sraxf/qual4_decode.c | 257 -
libs/sraxf/qual4_encode.c | 232 -
libs/sraxf/read-desc.c | 143 -
libs/sraxf/read-seg-from-readn.c | 361 -
libs/sraxf/rewrite-spot-name.c | 222 -
libs/sraxf/rotate.c | 271 -
libs/sraxf/spot-desc.c | 102 -
libs/sraxf/stats.c | 501 -
libs/sraxf/stats_quality.c | 132 -
libs/sraxf/swap.c | 228 -
libs/sraxf/tokenize-spot_name-454.c | 122 -
libs/sraxf/tokenize-spot_name-abi.c | 145 -
libs/sraxf/tokenize-spot_name-helicos.c | 111 -
libs/sraxf/tokenize-spot_name-illumina.c | 150 -
libs/sraxf/tokenize-spot_name-ion-torrent.c | 135 -
libs/sraxf/untyped-priv.h | 83 -
libs/sraxf/untyped.c | 378 -
libs/sraxf/v0-decompress-init.c | 2841 --
libs/sraxf/v0-decompress-local.h | 368 -
libs/sraxf/v0-decompress.c | 1096 -
libs/sraxf/v0-decompress.h | 170 -
libs/sraxf/v0-funcs.c | 337 -
libs/sraxf/varloc.c | 105 -
libs/vdb/Makefile | 180 -
libs/vdb/blob-headers.c | 726 -
libs/vdb/blob-headers.h | 114 -
libs/vdb/blob-priv.h | 200 -
libs/vdb/blob.c | 1569 -
libs/vdb/blob.h | 84 -
libs/vdb/cast.c | 583 -
libs/vdb/column-cmn.c | 307 -
libs/vdb/column-priv.h | 294 -
libs/vdb/column.c | 80 -
libs/vdb/compare.c | 242 -
libs/vdb/cursor-cmn.c | 2481 --
libs/vdb/cursor-priv.h | 311 -
libs/vdb/cursor.c | 200 -
libs/vdb/database-cmn.c | 724 -
libs/vdb/database-depend.c | 1807 --
libs/vdb/database-load.c | 119 -
libs/vdb/database-priv.h | 151 -
libs/vdb/database.c | 29 -
libs/vdb/dbmgr-cmn.c | 825 -
libs/vdb/dbmgr-priv.h | 115 -
libs/vdb/dbmgr.c | 148 -
libs/vdb/delta_average.c | 297 -
libs/vdb/environment-read.c | 108 -
libs/vdb/fixed-row-len.c | 67 -
libs/vdb/index_insert.c | 132 -
libs/vdb/index_lookup.c | 176 -
libs/vdb/index_project.c | 175 -
libs/vdb/libvdb.vers.h | 27 -
libs/vdb/libwvdb.vers.h | 27 -
libs/vdb/linker-cmn.c | 651 -
libs/vdb/linker-int.c | 665 -
libs/vdb/linker-priv.h | 271 -
libs/vdb/linker.c | 45 -
libs/vdb/merge.c | 215 -
libs/vdb/meta-append.c | 145 -
libs/vdb/meta-attr-read.c | 448 -
libs/vdb/meta-attr-write.c | 529 -
libs/vdb/meta-read.c | 140 -
libs/vdb/meta-value.c | 381 -
libs/vdb/meta-write.c | 155 -
libs/vdb/page-map.c | 1721 -
libs/vdb/page-map.h | 383 -
libs/vdb/parameter-read.c | 103 -
libs/vdb/phys-cmn.c | 679 -
libs/vdb/phys-load.c | 330 -
libs/vdb/phys-priv.h | 188 -
libs/vdb/phys.c | 67 -
libs/vdb/prod-cmn.c | 2321 --
libs/vdb/prod-expr.c | 887 -
libs/vdb/prod-expr.h | 202 -
libs/vdb/prod-func.c | 955 -
libs/vdb/prod-priv.h | 459 -
libs/vdb/prod.c | 136 -
libs/vdb/range-validate.c | 195 -
libs/vdb/redimension.c | 108 -
libs/vdb/report-vdb.c | 856 -
libs/vdb/row-id.c | 64 -
libs/vdb/row-len.c | 65 -
libs/vdb/schema-db.c | 746 -
libs/vdb/schema-dump.c | 683 -
libs/vdb/schema-dump.h | 208 -
libs/vdb/schema-eval.c | 1400 -
libs/vdb/schema-expr.c | 2169 --
libs/vdb/schema-expr.h | 396 -
libs/vdb/schema-func.c | 1657 -
libs/vdb/schema-int.c | 376 -
libs/vdb/schema-parse.c | 855 -
libs/vdb/schema-parse.h | 607 -
libs/vdb/schema-priv.h | 1308 -
libs/vdb/schema-prod.c | 1004 -
libs/vdb/schema-tbl.c | 2928 --
libs/vdb/schema-tok.c | 74 -
libs/vdb/schema-tok.h | 61 -
libs/vdb/schema-type.c | 2573 --
libs/vdb/schema.c | 1768 --
libs/vdb/split.c | 398 -
libs/vdb/table-cmn.c | 1247 -
libs/vdb/table-load.c | 323 -
libs/vdb/table-priv.h | 232 -
libs/vdb/table.c | 109 -
libs/vdb/transpose.c | 720 -
libs/vdb/wcolumn.c | 1069 -
libs/vdb/wcursor.c | 1205 -
libs/vdb/wdatabase.c | 661 -
libs/vdb/wdbmgr.c | 251 -
libs/vdb/wlinker.c | 96 -
libs/vdb/wphys.c | 909 -
libs/vdb/wprod.c | 439 -
libs/vdb/wtable.c | 987 -
libs/vdb/xform-priv.h | 83 -
libs/vfs/Makefile | 123 -
libs/vfs/keyring.c | 292 -
libs/vfs/keyring.h | 111 -
libs/vfs/manager.c | 3027 --
libs/vfs/path-priv.h | 147 -
libs/vfs/path.c | 3374 --
libs/vfs/resolver-priv.h | 144 -
libs/vfs/resolver.c | 4386 ---
libs/vfs/srapath-stub.c | 372 -
libs/vfs/srapath.c | 1424 -
libs/vfs/unix/syskeyring.c | 161 -
libs/vfs/unix/syspath.c | 149 -
libs/vfs/win/syskeyring.c | 58 -
libs/vfs/win/syspath.c | 343 -
libs/vxf/Makefile | 162 -
libs/vxf/add-row-id.c | 80 -
libs/vxf/bit_or.c | 135 -
libs/vxf/bunzip.c | 130 -
libs/vxf/bzip.c | 182 -
libs/vxf/ceil.c | 48 -
libs/vxf/checksum.c | 566 -
libs/vxf/clip.c | 200 -
libs/vxf/cut.c | 227 -
libs/vxf/delta.c | 108 -
libs/vxf/deriv.c | 111 -
libs/vxf/diff.c | 356 -
libs/vxf/echo.c | 187 -
libs/vxf/exists.c | 212 -
libs/vxf/extract_token.c | 105 -
libs/vxf/floor.c | 49 -
libs/vxf/fsplit-join.impl.h | 136 -
libs/vxf/funzip.c | 172 -
libs/vxf/fzip.c | 168 -
libs/vxf/integral.c | 115 -
libs/vxf/integral_0.c | 115 -
libs/vxf/irzip.c | 564 -
libs/vxf/irzip.impl.h | 482 -
libs/vxf/iunzip.c | 748 -
libs/vxf/izip-common.h | 195 -
libs/vxf/izip-decode.impl.h | 162 -
libs/vxf/izip-encode.impl.h | 523 -
libs/vxf/izip.c | 865 -
libs/vxf/lower-case-tech-reads.c | 111 -
libs/vxf/map.c | 1019 -
libs/vxf/math-funcs-impl.h | 361 -
libs/vxf/max.c | 175 -
libs/vxf/min.c | 175 -
libs/vxf/outlier-decoder.c | 114 -
libs/vxf/outlier-encoder.c | 142 -
libs/vxf/pack.c | 92 -
libs/vxf/paste.c | 357 -
libs/vxf/rand_4na_2na.c | 200 -
libs/vxf/rldecode.c | 155 -
libs/vxf/rlencode.c | 262 -
libs/vxf/round.c | 49 -
libs/vxf/simple-sub-select.c | 278 -
libs/vxf/sprintf.c | 1279 -
libs/vxf/strtonum.c | 354 -
libs/vxf/subtract-row-id.c | 83 -
libs/vxf/sum.c | 356 -
libs/vxf/trim.c | 229 -
libs/vxf/trunc.c | 49 -
libs/vxf/undelta.c | 108 -
libs/vxf/unpack.c | 115 -
libs/vxf/unzip.c | 234 -
libs/vxf/vec-sum.c | 239 -
libs/vxf/wgs-tokenize-accession.c | 212 -
libs/vxf/zip.c | 214 -
libs/wgsxf/Makefile | 124 -
libs/wgsxf/build_read_type.c | 113 -
libs/wgsxf/build_scaffold.c | 435 -
os-arch.perl | 35 +
os-arch.pm | 100 +
package.pm | 52 +
test/Makefile | 30 +
tools/.gitignore | 3 +
tools/Makefile | 31 +-
tools/align-info/Makefile | 5 +-
tools/align-info/align-info.c | 8 +-
tools/align-info/align-info.vers | 2 +-
tools/align-info/align-info.vers.h | 1 +
tools/bam-loader/Globals.h | 1 +
tools/bam-loader/Makefile | 30 +-
tools/bam-loader/alignment-writer.c | 85 +
tools/bam-loader/alignment-writer.h | 6 +-
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/bam-loader.c | 82 +-
tools/bam-loader/bam-loader3.c | 1028 +
tools/bam-loader/bam-reader.c | 1104 +
tools/bam-loader/bam-reader.h | 98 +
tools/bam-loader/loader-imp.c | 162 +-
tools/bam-loader/loader-imp3.c | 369 +
tools/bam-loader/loader-imp3.h | 38 +
tools/bam-loader/reference-writer.c | 85 +-
tools/bam-loader/reference-writer.h | 3 +-
tools/cache-mgr/Makefile | 4 +-
tools/cache-mgr/cache-mgr.c | 307 +-
tools/cache-mgr/cache-mgr.vers | 2 +-
tools/cache-mgr/cache-mgr.vers.h | 1 +
tools/ccextract/Makefile | 102 +
tools/ccextract/ccextract.c | 1283 +
tools/ccextract/ccextract.vers | 1 +
tools/cg-dump/Makefile | 117 +
tools/cg-dump/cg-dump.c | 1563 +
tools/cg-dump/cg-dump.vers | 1 +
tools/cg-dump/last_rowid.c | 353 +
tools/cg-dump/last_rowid.h | 44 +
tools/cg-dump/line_token_iter.c | 148 +
tools/cg-dump/line_token_iter.h | 66 +
tools/cg-dump/num-gen.c | 848 +
tools/{vdb-copy => cg-dump}/num-gen.h | 0
tools/cg-dump/progressbar.c | 140 +
tools/{vdb-copy => cg-dump}/progressbar.h | 0
tools/cg-dump/sg_lookup.c | 277 +
tools/cg-dump/sg_lookup.h | 65 +
tools/cg-load/.gitignore | 2 +
tools/cg-load/Makefile | 6 +-
tools/cg-load/cg-load.c | 14 +-
tools/cg-load/cg-load.vers | 2 +-
tools/cg-load/factory-tag-lfr.c | 261 +
tools/cg-load/factory-tag-lfr.h | 37 +
tools/cg-load/writer-algn.c | 8 +-
tools/cg-load/writer-evidence-dnbs.c | 5 +-
tools/cg-load/writer-evidence-intervals.c | 15 +-
tools/check-blob-size/Makefile | 103 +
tools/check-blob-size/check-blob-size.c | 332 +
tools/check-blob-size/check-blob-size.vers | 1 +
tools/copycat/Makefile | 109 +
tools/copycat/ccbuffer.c | 153 +
tools/copycat/ccbuffermgr.c | 234 +
tools/copycat/ccbufferq.c | 175 +
tools/copycat/cccat.c | 1797 ++
tools/copycat/cccopier.c | 217 +
tools/copycat/cccopy.c | 347 +
tools/copycat/ccfile.c | 271 +
tools/copycat/ccfileformat.c | 383 +
tools/copycat/ccproc.c | 319 +
tools/copycat/ccprocone.c | 217 +
tools/copycat/ccread.c | 302 +
tools/copycat/ccsra.c | 1239 +
tools/copycat/ccsubchunk.c | 390 +
tools/copycat/cctar.c | 2199 ++
tools/copycat/cctree-dump.c | 1030 +
tools/copycat/cctree-priv.h | 351 +
tools/copycat/cctree.c | 754 +
tools/copycat/copycat-priv.h | 229 +
tools/copycat/copycat.c | 1263 +
tools/copycat/copycat.vers | 1 +
tools/copycat/debug.h | 75 +
tools/deseq/Makefile | 102 +
tools/deseq/csra-trim.vers | 1 +
tools/deseq/deseq.c | 521 +
tools/fastq-dump/Makefile | 106 +
tools/fastq-dump/args.cpp | 622 +
tools/fastq-dump/args.hpp | 330 +
tools/fastq-dump/fastq-dump.cpp | 633 +
tools/fastq-dump/fastq-dump.vers | 1 +
tools/fastq-dump/filters.cpp | 300 +
tools/fastq-dump/filters.hpp | 114 +
tools/fastq-dump/koutstream | 281 +
tools/fastq-loader/.gitignore | 1 +
tools/fastq-loader/Makefile | 13 +-
tools/fastq-loader/fastq-grammar.c | 454 +-
tools/fastq-loader/fastq-grammar.y | 421 +-
tools/fastq-loader/fastq-lex.c | 374 +-
tools/fastq-loader/fastq-lex.l | 215 +-
tools/fastq-loader/fastq-tokens.h | 21 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/fastq-loader/latf-load.vers.h | 1 +
tools/fastq-loader/loader-imp.c | 11 +-
tools/fix-run-stat/Makefile | 93 +
tools/fix-run-stat/fix-run-stat.c | 355 +
tools/fix-run-stat/fix-run-stat.vers | 1 +
tools/fuse/Makefile | 179 +
tools/fuse/accessor.c | 134 +
tools/fuse/accessor.h | 46 +
tools/fuse/debug.h | 53 +
tools/fuse/directory.c | 566 +
tools/fuse/directory.h | 34 +
tools/fuse/dump-idx.c | 107 +
tools/fuse/dump-idx.vers | 1 +
tools/fuse/dump-idx.vers.h | 1 +
tools/fuse/file.c | 275 +
tools/fuse/file.h | 33 +
tools/fuse/formats.c | 443 +
tools/fuse/formats.h | 157 +
tools/fuse/kfile-accessor.c | 73 +
tools/fuse/kfile-accessor.h | 33 +
tools/fuse/log.c | 196 +
tools/fuse/log.h | 53 +
tools/fuse/node.c | 273 +
tools/fuse/node.h | 108 +
tools/fuse/remote-cache.c | 1538 +
tools/fuse/remote-cache.h | 169 +
tools/fuse/remote-directory.c | 411 +
tools/fuse/remote-directory.h | 33 +
tools/fuse/remote-file.c | 300 +
tools/fuse/remote-file.h | 33 +
tools/fuse/remote-fuser.c | 212 +
tools/fuse/remote-fuser.h | 52 +
tools/fuse/remote-fuser.vers | 1 +
tools/fuse/remote-link.c | 208 +
tools/fuse/remote-link.h | 33 +
tools/fuse/remote-xml.c | 603 +
tools/fuse/remote-xml.h | 59 +
tools/fuse/sra-directory.c | 107 +
tools/fuse/sra-directory.h | 33 +
tools/fuse/sra-fastq.c | 245 +
tools/fuse/sra-fastq.h | 34 +
tools/fuse/sra-fuser-test.c | 100 +
tools/fuse/sra-fuser-test.vers | 1 +
tools/fuse/sra-fuser-test.vers.h | 1 +
tools/fuse/sra-fuser.c | 201 +
tools/fuse/sra-fuser.h | 48 +
tools/fuse/sra-fuser.vers | 1 +
tools/fuse/sra-fuser.xsd | 207 +
tools/fuse/sra-list.c | 1225 +
tools/fuse/sra-list.h | 86 +
tools/fuse/sra-makeidx.c | 960 +
tools/fuse/sra-makeidx.vers | 1 +
tools/fuse/sra-node.c | 165 +
tools/fuse/sra-node.h | 34 +
tools/fuse/sra-sff.c | 249 +
tools/fuse/sra-sff.h | 34 +
tools/fuse/tar-file.c | 127 +
tools/fuse/tar-file.h | 33 +
tools/fuse/tar-list.c | 598 +
tools/fuse/tar-list.h | 49 +
tools/fuse/tar-node.c | 320 +
tools/fuse/tar-node.h | 35 +
tools/fuse/text-file.c | 134 +
tools/fuse/text-file.h | 36 +
tools/fuse/unix/remote-fuser-sys.c | 696 +
tools/fuse/unix/sra-fuser-sys.c | 634 +
tools/fuse/xml.c | 516 +
tools/fuse/xml.h | 60 +
tools/fuse/zlib-simple.c | 65 +
tools/fuse/zlib-simple.h | 33 +
tools/kar/Makefile | 6 +-
tools/kar/kar.c | 8 +-
tools/kar/kar.vers | 2 +-
tools/kar/kar.vers.h | 1 +
tools/kar/sra-kar.c | 10 +-
tools/kar/sra-kar.vers | 2 +-
tools/kar/sra-kar.vers.h | 1 +
tools/keyring-srv/Makefile | 106 +
tools/keyring-srv/keyring-data.c | 346 +
tools/keyring-srv/keyring-data.h | 130 +
tools/keyring-srv/keyring-database.c | 441 +
tools/keyring-srv/keyring-database.h | 45 +
tools/keyring-srv/keyring-srv-main.c | 340 +
tools/keyring-srv/keyring-srv.c | 522 +
tools/keyring-srv/keyring-srv.h | 101 +
tools/keyring-srv/keyring-srv.vers | 1 +
tools/kqsh/.gitignore | 7 +
tools/kqsh/Makefile | 221 +
tools/kqsh/kqsh-alter.c | 347 +
tools/kqsh/kqsh-close.c | 186 +
tools/kqsh/kqsh-create.c | 680 +
tools/kqsh/kqsh-help.c | 1292 +
tools/kqsh/kqsh-load.c | 410 +
tools/kqsh/kqsh-open.c | 199 +
tools/kqsh/kqsh-parse.c | 198 +
tools/kqsh/kqsh-print.c | 170 +
tools/kqsh/kqsh-priv.h | 151 +
tools/kqsh/kqsh-show.c | 290 +
tools/kqsh/kqsh-thunk.pl | 662 +
tools/kqsh/kqsh-tok.c | 99 +
tools/kqsh/kqsh-tok.h | 155 +
tools/kqsh/kqsh-write.c | 321 +
tools/kqsh/kqsh.c | 530 +
tools/kqsh/kqsh.vers | 1 +
tools/meta-sync/Makefile | 114 +
tools/meta-sync/meta-sync.c | 1517 +
tools/meta-sync/meta-sync.pl | 41 +
tools/meta-sync/meta-sync.vers | 1 +
tools/nenctool/Makefile | 12 +-
tools/nenctool/nenctest.c | 4 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.c | 4 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/Makefile | 2 +-
tools/nencvalid/nencvalid.c | 2 +-
tools/nencvalid/nencvalid.vers | 2 +-
tools/pacbio-load/.gitignore | 7 +
tools/pacbio-load/Makefile | 140 +
tools/pacbio-load/pacbio-load.c | 638 +
tools/pacbio-load/pacbio-load.vers | 1 +
tools/pacbio-load/pl-basecalls_cmn.c | 97 +
tools/pacbio-load/pl-basecalls_cmn.h | 60 +
tools/pacbio-load/pl-consensus.c | 413 +
tools/pacbio-load/pl-consensus.h | 83 +
tools/pacbio-load/pl-context.c | 211 +
tools/pacbio-load/pl-context.h | 87 +
tools/pacbio-load/pl-metrics.c | 779 +
tools/pacbio-load/pl-metrics.h | 83 +
tools/pacbio-load/pl-passes.c | 437 +
tools/pacbio-load/pl-passes.h | 70 +
tools/pacbio-load/pl-progress.c | 195 +
tools/pacbio-load/pl-progress.h | 70 +
tools/pacbio-load/pl-regions.c | 1048 +
tools/pacbio-load/pl-regions.h | 140 +
tools/pacbio-load/pl-sequence.c | 928 +
tools/pacbio-load/pl-sequence.h | 110 +
tools/pacbio-load/pl-tools.c | 616 +
tools/pacbio-load/pl-tools.h | 291 +
tools/pacbio-load/pl-zmw.c | 221 +
tools/pacbio-load/pl-zmw.h | 105 +
tools/pacbio-load/verify/ins_nl.pl | 15 +
tools/pacbio-load/verify/ins_nl_1.pl | 30 +
tools/pacbio-load/verify/ins_nl_2.pl | 24 +
tools/pacbio-load/verify/ins_nl_4.pl | 24 +
tools/pacbio-load/verify/ins_nl_f.pl | 27 +
tools/prefetch/Makefile | 22 +-
tools/prefetch/prefetch.c | 99 +-
tools/prefetch/prefetch.vers | 2 +-
tools/prefetch/prefetch.vers.h | 1 +
tools/qual-recal/Makefile | 101 +
tools/qual-recal/make_histo_data.sh | 12 +
tools/qual-recal/qual-recal.c | 654 +
tools/qual-recalib-stat/.gitignore | 3 +
tools/qual-recalib-stat/Makefile | 100 +
tools/qual-recalib-stat/columns.c | 94 +
tools/qual-recalib-stat/columns.h | 67 +
tools/qual-recalib-stat/context.c | 330 +
tools/qual-recalib-stat/context.h | 120 +
tools/qual-recalib-stat/fasta_dump.pl | 81 +
.../namelist_tools.c | 0
tools/qual-recalib-stat/namelist_tools.h | 53 +
tools/qual-recalib-stat/num-gen.c | 848 +
tools/{vdb-copy => qual-recalib-stat}/num-gen.h | 0
tools/qual-recalib-stat/progressbar.c | 182 +
tools/qual-recalib-stat/progressbar.h | 75 +
tools/qual-recalib-stat/qual-recalib-stat.c | 421 +
tools/qual-recalib-stat/qual-recalib-stat.vers | 1 +
tools/qual-recalib-stat/qual-recalib-stat.vers.h | 1 +
tools/qual-recalib-stat/reader.c | 241 +
tools/qual-recalib-stat/reader.h | 88 +
tools/qual-recalib-stat/ref_exclude.c | 561 +
tools/qual-recalib-stat/ref_exclude.h | 71 +
tools/qual-recalib-stat/ref_grab.pl | 82 +
tools/qual-recalib-stat/spot_position.c | 121 +
tools/qual-recalib-stat/spot_position.h | 68 +
tools/qual-recalib-stat/stat_mod.c | 883 +
tools/qual-recalib-stat/stat_mod.h | 148 +
tools/qual-recalib-stat/stat_mod_1.c | 962 +
tools/qual-recalib-stat/stat_mod_1.h | 160 +
tools/qual-recalib-stat/stat_mod_2.c | 1041 +
tools/qual-recalib-stat/stat_mod_2.h | 141 +
tools/qual-recalib-stat/writer.c | 436 +
tools/qual-recalib-stat/writer.h | 80 +
tools/rd-filter-redact/Makefile | 122 +
tools/rd-filter-redact/rd-filter-redact.c | 1355 +
tools/rd-filter-redact/rd-filter-redact.vers | 1 +
tools/rd-filter-redact/read-filter-redact.c | 865 +
tools/rd-filter-redact/read-filter-redact.vers | 1 +
tools/rd-filter-redact/read-filter-redact.vers.h | 1 +
tools/rd-filter-redact/test-read-write-cursor.c | 222 +
tools/rd-filter-redact/test-read-write-cursor.vers | 1 +
tools/run-stat/.gitignore | 6 +
tools/run-stat/Makefile | 120 +
tools/run-stat/chart.c | 465 +
tools/run-stat/chart.h | 109 +
tools/run-stat/context.c | 439 +
tools/run-stat/context.h | 98 +
tools/run-stat/definitions.h | 78 +
tools/run-stat/helper.c | 715 +
tools/run-stat/helper.h | 126 +
tools/run-stat/key_value.c | 549 +
tools/run-stat/key_value.h | 64 +
tools/run-stat/mod_cmn.c | 329 +
tools/run-stat/mod_cmn.h | 149 +
tools/run-stat/mod_reads.c | 747 +
tools/run-stat/mod_reads.h | 42 +
tools/run-stat/mod_reads_defs.h | 128 +
tools/run-stat/mod_reads_helper.c | 575 +
tools/run-stat/mod_reads_helper.h | 61 +
tools/run-stat/num-gen.c | 497 +
tools/run-stat/num-gen.h | 81 +
tools/run-stat/progressbar.c | 191 +
tools/run-stat/progressbar.h | 76 +
tools/run-stat/rd_filter.c | 243 +
tools/run-stat/rd_filter.h | 98 +
tools/run-stat/run-stat.c | 703 +
tools/run-stat/run-stat.vers | 1 +
tools/run-stat/svg.c | 753 +
tools/run-stat/svg.h | 117 +
tools/sam-dump/Makefile | 3 +-
tools/sam-dump/sam-dump.c | 28 +-
tools/sam-dump/sam-dump.vers | 2 +-
tools/sra-dbcc/Makefile | 4 +-
tools/sra-dbcc/sra-dbcc.c | 36 +-
tools/sra-dbcc/sra-dbcc.vers | 2 +-
tools/sra-dump/.gitignore | 1 +
tools/sra-dump/Makefile | 5 +-
tools/sra-dump/abi-dump.vers | 2 +-
tools/sra-dump/abi-dump.vers.h | 1 +
tools/sra-dump/abi.c | 2 +-
tools/sra-dump/core.c | 23 +-
tools/sra-dump/factory.c | 8 +-
tools/sra-dump/factory.h | 2 +-
tools/sra-dump/fastq-dump.vers | 2 +-
tools/sra-dump/fastq-dump.vers.h | 1 +
tools/sra-dump/fastq.c | 2 +-
tools/sra-dump/illumina-dump.vers | 2 +-
tools/sra-dump/illumina-dump.vers.h | 1 +
tools/sra-dump/illumina.c | 60 +-
tools/sra-dump/sff-dump.vers | 2 +-
tools/sra-dump/sff-dump.vers.h | 1 +
tools/sra-dump/sra-dump.c | 2 +-
tools/sra-dump/sra-dump.vers | 2 +-
tools/sra-load/Makefile | 22 +-
tools/sra-load/abi-load.vers | 2 +-
tools/sra-load/common-xml.c | 8 +-
tools/sra-load/experiment-xml.c | 2 +-
tools/sra-load/fastq-load.vers | 2 +-
tools/sra-load/helicos-load.vers | 2 +-
tools/sra-load/illumina-load.vers | 2 +-
tools/sra-load/loader.c | 8 +-
tools/sra-load/pacbio-fmt.c | 146 +
tools/sra-load/pacbio-loadxml.vers | 2 +-
tools/sra-load/run-xml.c | 24 +-
tools/sra-load/sff-fmt.c | 2 +-
tools/sra-load/sff-load.vers | 2 +-
tools/sra-load/sra-writer.c | 8 +-
tools/sra-load/srf-fmt.c | 4 +-
tools/sra-load/srf-illumina.c | 2 +-
tools/sra-load/srf-load.vers | 2 +-
tools/sra-load/writer-illumina.c | 17 +-
tools/sra-pileup/.gitignore | 2 +
tools/sra-pileup/4na_ascii.c | 95 +
tools/sra-pileup/4na_ascii.h | 44 +
tools/sra-pileup/Makefile | 51 +-
tools/sra-pileup/cg_tools.c | 807 +-
tools/sra-pileup/cg_tools.h | 21 +-
tools/sra-pileup/cmdline_cmn.c | 29 +-
tools/sra-pileup/cmdline_cmn.h | 21 +-
tools/sra-pileup/dyn_string.c | 186 +
tools/sra-pileup/dyn_string.h | 54 +
tools/sra-pileup/inputfiles.c | 2 +-
tools/sra-pileup/make_opt.pl | 13 +
tools/sra-pileup/perf_log.c | 273 +
tools/sra-pileup/perf_log.h | 52 +
tools/sra-pileup/pileup_counters.c | 447 +
tools/sra-pileup/pileup_counters.h | 41 +
tools/sra-pileup/pileup_index.c | 122 +
tools/sra-pileup/pileup_index.h | 40 +
tools/sra-pileup/pileup_options.h | 61 +
tools/sra-pileup/pileup_stat.c | 391 +
tools/sra-pileup/pileup_stat.h | 40 +
tools/sra-pileup/pileup_v2.c | 382 +
tools/sra-pileup/pileup_v2.h | 40 +
tools/sra-pileup/pileup_varcount.c | 139 +
tools/sra-pileup/pileup_varcount.h | 40 +
tools/sra-pileup/read_fkt.c | 1436 +-
tools/sra-pileup/ref_regions.c | 374 +-
tools/sra-pileup/ref_regions.h | 29 +-
tools/sra-pileup/ref_walker.c | 283 +-
tools/sra-pileup/ref_walker.h | 37 +-
tools/sra-pileup/ref_walker_0.c | 223 +
tools/sra-pileup/ref_walker_0.h | 107 +
tools/sra-pileup/report_deletes.c | 259 +
tools/sra-pileup/report_deletes.h | 41 +
tools/sra-pileup/reref.c | 11 +-
tools/sra-pileup/rna_splice_log.c | 374 +
tools/sra-pileup/rna_splice_log.h | 87 +
tools/sra-pileup/sam-aligned.c | 4430 +--
tools/sra-pileup/sam-aligned.h | 5 +-
tools/sra-pileup/sam-dump-opts.c | 107 +-
tools/sra-pileup/sam-dump-opts.h | 26 +-
tools/sra-pileup/sam-dump.c | 52 +-
tools/sra-pileup/sam-dump.vers | 2 +-
tools/sra-pileup/sam-dump.vers.h | 1 +
tools/sra-pileup/sam-dump2.vers | 1 +
tools/sra-pileup/sam-dump3.c | 28 +-
.../bam-load.3.vers => sra-pileup/sam-dump3.vers} | 0
tools/sra-pileup/sam-hdr.c | 15 +-
tools/sra-pileup/sam-unaligned.c | 221 +-
tools/sra-pileup/sam-unaligned.h | 5 +-
tools/sra-pileup/splitfastq.pl | 46 +
tools/sra-pileup/sra-pileup.c | 1872 +-
tools/sra-pileup/sra-pileup.vers | 2 +-
tools/sra-pileup/sra-pileup.vers.h | 1 +
tools/sra-pileup/walk_debug.c | 88 +
tools/sra-pileup/walk_debug.h | 42 +
tools/sra-pileup/writer.c | 137 +
tools/sra-pileup/writer.h | 32 +
tools/sra-shell/Makefile | 58 +
tools/sra-shell/guilib/Makefile | 71 +
tools/sra-shell/job-exec/Makefile | 71 +
tools/sra-shell/parser/Makefile | 71 +
tools/sra-shell/parser/sra-shell-lex.l | 103 +
tools/sra-shell/parser/sra-shell.y | 54 +
tools/sra-shell/sra-gui/Makefile | 94 +
tools/sra-shell/sra-gui/sra-gui.c | 56 +
tools/sra-shell/sra-gui/sra-gui.vers | 1 +
tools/sra-shell/sra-shell/Makefile | 101 +
tools/sra-shell/sra-shell/sra-shell.c | 56 +
tools/sra-shell/sra-shell/sra-shell.vers | 1 +
tools/sra-shell/turboVision/Makefile | 71 +
tools/sra-sort/Makefile | 21 +-
tools/sra-sort/col-pair.c | 4 +-
tools/sra-sort/csra-tbl.c | 6 +-
tools/sra-sort/db-pair.c | 12 +-
tools/sra-sort/dir-pair.c | 14 +-
tools/sra-sort/dump-blob-boundaries.c | 6 +-
tools/sra-sort/meta-pair.c | 4 +-
tools/sra-sort/run.c | 14 +-
tools/sra-sort/sort-defs.h | 12 +
tools/sra-sort/sra-sort.c | 4 +-
tools/sra-sort/sra-sort.vers | 2 +-
tools/sra-sort/tbl-pair.c | 2 +-
tools/sra-stat/Makefile | 6 +-
tools/sra-stat/sra-stat.c | 132 +-
tools/sra-stat/sra-stat.vers | 2 +-
tools/sra-stat/sra-stat.vers.h | 1 +
tools/sra/Makefile | 109 +
tools/sra/sra-dbcc.c | 442 +
tools/sra/table-vers.c | 236 +
tools/sra/table-vers.vers | 1 +
tools/srapath/Makefile | 5 +-
tools/srapath/srapath.c | 4 +-
tools/srapath/srapath.vers | 2 +-
tools/srapath/srapath.vers.h | 1 +
tools/update-schema/Makefile | 102 +
tools/update-schema/update-schema.c | 452 +
tools/update-schema/vdb-update-schema.vers | 1 +
tools/util/Makefile | 170 +-
tools/util/crc32sum.c | 279 +
tools/util/kdbmeta.c | 43 +-
tools/util/kdbmeta.vers | 2 +-
tools/util/kdbmeta.vers.h | 1 +
tools/util/md5cp.c | 714 +
tools/util/md5cp.vers | 2 +-
tools/util/md5cp.vers.h | 1 +
tools/util/pacbio-correct.c | 221 +
tools/util/pacbio-correct.vers | 1 +
tools/util/rcexplain.c | 6 +-
tools/util/rcexplain.vers | 2 +-
tools/util/rcexplain.vers.h | 1 +
tools/util/rowwritetest.c | 4 +-
tools/util/rowwritetest.vers | 2 +-
tools/util/schema-replace.c | 394 +
tools/util/schema-replace.sh | 22 +
tools/util/schema-replace.vers | 2 +-
tools/util/schema-replace.vers.h | 1 +
tools/util/sortreadtest.c | 355 +
tools/util/test-sra.c | 26 +-
tools/util/test-sra.vers | 2 +-
tools/util/test-sra.vers.h | 1 +
tools/util/testld.vers | 2 +-
tools/util/txt2kdb.c | 6 +-
tools/util/txt2kdb.vers | 2 +-
tools/util/vdb-lock.c | 2 +-
tools/util/vdb-lock.vers | 2 +-
tools/util/vdb-lock.vers.h | 1 +
tools/util/vdb-passwd.vers | 2 +-
tools/util/vdb-passwd.vers.h | 1 +
tools/util/vdb-unlock.c | 2 +-
tools/util/vdb-unlock.vers | 2 +-
tools/util/vdb-unlock.vers.h | 1 +
tools/util/win/PrintOS.c | 2 +-
tools/util/win/syspass.c | 2 +-
tools/vcf-loader/Makefile | 118 +
tools/vcf-loader/vcf-database.c | 165 +
tools/vcf-loader/vcf-database.h | 40 +
tools/vcf-loader/vcf-grammar.c | 1686 +
tools/vcf-loader/vcf-grammar.h | 61 +
tools/vcf-loader/vcf-grammar.y | 123 +
tools/vcf-loader/vcf-lex.c | 2516 ++
tools/vcf-loader/vcf-lex.l | 134 +
tools/vcf-loader/vcf-load.vers | 1 +
tools/vcf-loader/vcf-loader.c | 131 +
tools/vcf-loader/vcf-parse.h | 88 +
tools/vcf-loader/vcf-reader.c | 438 +
tools/vcf-loader/vcf-reader.h | 110 +
tools/vdb-config/Makefile | 20 +-
tools/vdb-config/configure.cpp | 781 +
tools/vdb-config/configure.h | 49 +
tools/vdb-config/interactive.cpp | 1048 +
tools/vdb-config/interactive.h | 50 +
tools/vdb-config/util.cpp | 1096 +
tools/vdb-config/util.hpp | 699 +
tools/vdb-config/vdb-config-model.cpp | 428 +
tools/vdb-config/vdb-config-model.hpp | 433 +
tools/vdb-config/vdb-config.c | 364 +-
tools/vdb-config/vdb-config.vers | 2 +-
tools/vdb-config/vdb-config.vers.h | 1 +
tools/vdb-config/vdb-config2.cpp | 30 +
tools/vdb-config/vdb-config2.h | 29 +
tools/vdb-copy/.gitignore | 17 +
tools/vdb-copy/Makefile | 5 +-
tools/vdb-copy/coldefs.c | 8 +-
tools/vdb-copy/column_match.c | 31 +
tools/vdb-copy/column_match.h | 42 +
tools/vdb-copy/copy_context.c | 47 +
tools/vdb-copy/copy_context.h | 58 +
tools/vdb-copy/copy_meta.c | 6 +-
tools/vdb-copy/get_platform.c | 336 +-
tools/vdb-copy/get_platform.h | 92 +-
tools/vdb-copy/helper.c | 8 +-
tools/vdb-copy/type_matcher.c | 14 +-
tools/vdb-copy/vdb-copy.c | 18 +-
tools/vdb-copy/vdb-copy.kfg | 8 +-
tools/vdb-copy/vdb-copy.vers | 2 +-
tools/vdb-copy/vdb-copy.vers.h | 1 +
tools/vdb-decrypt/Makefile | 6 +-
tools/vdb-decrypt/shared.c | 32 +-
tools/vdb-decrypt/vdb-decrypt.vers | 2 +-
tools/vdb-decrypt/vdb-decrypt.vers.h | 1 +
tools/vdb-decrypt/vdb-encrypt.c | 4 +-
tools/vdb-decrypt/vdb-encrypt.vers | 2 +-
tools/vdb-decrypt/vdb-encrypt.vers.h | 1 +
tools/vdb-dump/.gitignore | 2 +
tools/vdb-dump/Makefile | 10 +-
tools/vdb-dump/help.txt | 272 +
tools/vdb-dump/vdb-boot.c | 448 +
tools/vdb-dump/vdb-boot.vers | 1 +
tools/vdb-dump/vdb-boot.vschema | 52 +
tools/vdb-dump/vdb-dump-bin.c | 1277 +
tools/vdb-dump/vdb-dump-bin.h | 44 +
tools/vdb-dump/vdb-dump-coldefs.c | 42 +-
tools/vdb-dump/vdb-dump-coldefs.h | 3 +
tools/vdb-dump/vdb-dump-context.c | 69 +-
tools/vdb-dump/vdb-dump-context.h | 11 +-
tools/vdb-dump/vdb-dump-fastq.c | 8 +-
tools/vdb-dump/vdb-dump-helper.c | 82 +-
tools/vdb-dump/vdb-dump-helper.h | 8 +-
tools/vdb-dump/vdb-dump-num-gen.c | 29 +
tools/vdb-dump/vdb-dump-num-gen.h | 2 +
tools/vdb-dump/vdb-dump-print.c | 550 +
tools/vdb-dump/vdb-dump-print.h | 73 +
tools/vdb-dump/vdb-dump.c | 222 +-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-dump/vdb-dump.vers.h | 1 +
tools/vdb-dump/vdb_info.c | 1205 +
tools/vdb-dump/vdb_info.h | 47 +
tools/vdb-validate/Makefile | 5 +-
tools/vdb-validate/vdb-validate.c | 729 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
tools/vdb-validate/vdb-validate.vers.h | 1 +
tools/vdbview/b_first.png | Bin 0 -> 528 bytes
tools/vdbview/b_goto.png | Bin 0 -> 475 bytes
tools/vdbview/b_last.png | Bin 0 -> 519 bytes
tools/vdbview/b_next.png | Bin 0 -> 428 bytes
tools/vdbview/b_nextpage.png | Bin 0 -> 639 bytes
tools/vdbview/b_prev.png | Bin 0 -> 426 bytes
tools/vdbview/b_prevpage.png | Bin 0 -> 636 bytes
tools/vdbview/b_search.png | Bin 0 -> 614 bytes
tools/vdbview/background.pas | 277 +
tools/vdbview/buttons.svg | 268 +
tools/vdbview/columnsel.lfm | 90 +
tools/vdbview/columnsel.pas | 115 +
tools/vdbview/dataproxy.pas | 602 +
tools/vdbview/gotoform.lfm | 56 +
tools/vdbview/gotoform.pas | 47 +
tools/vdbview/jobdef.pas | 27 +
tools/vdbview/linkedlist.pas | 186 +
tools/vdbview/logo_128.png | Bin 0 -> 1752 bytes
tools/vdbview/logo_16.png | Bin 0 -> 368 bytes
tools/vdbview/logo_256.png | Bin 0 -> 3524 bytes
tools/vdbview/logo_32.png | Bin 0 -> 541 bytes
tools/vdbview/logo_64.png | Bin 0 -> 910 bytes
tools/vdbview/mainwindow.lfm | 973 +
tools/vdbview/mainwindow.pas | 793 +
tools/vdbview/searchform.lfm | 69 +
tools/vdbview/searchform.pas | 79 +
tools/vdbview/selector_types.pas | 20 +
tools/vdbview/support_unit.pas | 217 +
tools/vdbview/svdb.pas | 676 +
tools/vdbview/svdb_obj.pas | 339 +
tools/vdbview/vdbview.ico | Bin 0 -> 25890 bytes
tools/vdbview/vdbview.lpi | 343 +
tools/vdbview/vdbview.lpr | 24 +
tools/vdbview/vdbview.res | Bin 0 -> 27156 bytes
tools/vdbview/vdbview1.ico | Bin 0 -> 25890 bytes
tools/vdbview/version.lfm | 40 +
tools/vdbview/version.pas | 33 +
tools/vtblcp/Makefile | 97 +
tools/vtblcp/vtblcp-priv.h | 40 +
tools/vtblcp/vtblcp.c | 979 +
tools/vtblcp/vtblcp.vers | 1 +
tools/workspace/.gitignore | 3 +
tools/workspace/Makefile | 125 +
tools/workspace/path-to-kar-file.cpp | 117 +
tools/workspace/prefs-lex.l | 181 +
tools/workspace/prefs-yacc.y | 189 +
tools/workspace/sra.cpp | 1514 +
tools/workspace/sra.vers | 1 +
tools/workspace/sratoolkit-exception.cpp | 126 +
tools/workspace/sratoolkit-exception.hpp | 111 +
tools/workspace/token.c | 228 +
tools/workspace/token.h | 99 +
tools/workspace/workspace.cpp | 1116 +
win-configure.bat | 1 +
1823 files changed, 132444 insertions(+), 527383 deletions(-)
create mode 100644 CHANGES
create mode 100644 GNU-license.txt
create mode 100644 README-blastn
create mode 100644 README-build
delete mode 100644 README-build.txt
create mode 100644 README-vdb-config.txt
create mode 100644 README-wget.txt
create mode 100644 README.md
create mode 100644 USAGE
create mode 100644 build/.gitignore
delete mode 100644 build/BUILD.linux
delete mode 100644 build/BUILD.mac
delete mode 100644 build/BUILD.win
delete mode 100644 build/COMP.linux
delete mode 100644 build/COMP.mac
delete mode 100644 build/COMP.win
delete mode 100644 build/LNKG.linux
delete mode 100644 build/LNKG.mac
delete mode 100644 build/LNKG.win
create mode 100644 build/MSVC/2010/.gitignore
create mode 100644 build/MSVC/2010/abi-dump.vcxproj
create mode 100644 build/MSVC/2010/align-info.vcxproj
create mode 100644 build/MSVC/2010/cache-mgr.vcxproj
create mode 100644 build/MSVC/2010/dll-project.props
create mode 100644 build/MSVC/2010/exe-project.props
create mode 100644 build/MSVC/2010/fastq-dump-ngs.vcxproj
create mode 100644 build/MSVC/2010/fastq-dump.vcxproj
create mode 100644 build/MSVC/2010/fastq-loader.vcxproj
create mode 100644 build/MSVC/2010/illumina-diump.vcxproj
create mode 100644 build/MSVC/2010/kar.vcxproj
create mode 100644 build/MSVC/2010/kdbmeta.vcxproj
create mode 100644 build/MSVC/2010/lib-project.props
create mode 100644 build/MSVC/2010/md5cp.vcxproj
create mode 100644 build/MSVC/2010/prefetch.vcxproj
create mode 100644 build/MSVC/2010/qual-recalib-stat.vcxproj
create mode 100644 build/MSVC/2010/rcexplain.vcxproj
create mode 100644 build/MSVC/2010/read-filter-redact.vcxproj
create mode 100644 build/MSVC/2010/sam-dump.vcxproj
create mode 100644 build/MSVC/2010/schema-replace.vcxproj
create mode 100644 build/MSVC/2010/sff-dump.vcxproj
create mode 100644 build/MSVC/2010/sra-kar.vcxproj
create mode 100644 build/MSVC/2010/sra-pileup.vcxproj
create mode 100644 build/MSVC/2010/sra-stat.vcxproj
create mode 100644 build/MSVC/2010/sra-tools.sln
create mode 100644 build/MSVC/2010/srapath.vcxproj
create mode 100644 build/MSVC/2010/test-project.props
create mode 100644 build/MSVC/2010/test-sra.vcxproj
create mode 100644 build/MSVC/2010/vcf-loader.vcxproj
create mode 100644 build/MSVC/2010/vdb-common.props
create mode 100644 build/MSVC/2010/vdb-config.vcxproj
create mode 100644 build/MSVC/2010/vdb-copy.vcxproj
create mode 100644 build/MSVC/2010/vdb-decrypt.vcxproj
create mode 100644 build/MSVC/2010/vdb-dump.vcxproj
create mode 100644 build/MSVC/2010/vdb-encrypt.vcxproj
create mode 100644 build/MSVC/2010/vdb-lock.vcxproj
create mode 100644 build/MSVC/2010/vdb-passwd.vcxproj
create mode 100644 build/MSVC/2010/vdb-unlock.vcxproj
create mode 100644 build/MSVC/2010/vdb-validate.vcxproj
create mode 100644 build/Makefile.cc
create mode 100644 build/Makefile.install
create mode 100644 build/Makefile.scm
create mode 100644 build/Makefile.sun
create mode 100644 build/Makefile.sun.cc
create mode 100644 build/Makefile.sun.gcc
create mode 100644 build/Xcode/asm-trace/asm-trace.xcodeproj/project.pbxproj
create mode 100644 build/Xcode/old-toolkit/.gitignore
create mode 100644 build/Xcode/old-toolkit/old-toolkit.xcodeproj/project.pbxproj
create mode 100755 build/cp.sh
create mode 100755 build/gprof2dot.py
mode change 100755 => 100644 build/ld.linux.cmn.sh
copy build/{ld.mac.gcc.sh => ld.mac.clang.sh} (100%)
mode change 100755 => 100644 build/ld.mac.cmn.sh
create mode 100755 build/ld.rwin.dlib.sh
create mode 100755 build/ld.rwin.exe.sh
create mode 100755 build/ld.rwin.slib.sh
create mode 100755 build/ld.rwin.stub.sh
create mode 100755 build/ld.rwin.vc++.sh
create mode 100644 build/ld.sun.cc.sh
create mode 100755 build/ld.sun.cmn.sh
create mode 100755 build/ld.sun.dlib.sh
create mode 100755 build/ld.sun.exe.sh
create mode 100644 build/ld.sun.ln.sh
create mode 100755 build/ld.sun.slib.sh
mode change 100755 => 100644 build/ld.unix.cmn.sh
mode change 100755 => 100644 build/ld.unix.slib.sh
create mode 100644 build/libexists.sh
create mode 100755 build/make-defs-xf.pl
create mode 100755 build/make-defs.pl
create mode 100755 build/run_remotely.sh
create mode 100755 build/scm-collect.sh
create mode 100755 build/scm.sh
create mode 100644 build/scm.txt
create mode 100755 build/sun-c++.sh
create mode 100755 build/sun-cc.sh
create mode 100755 build/tag-module.sh
create mode 100755 build/wait_for_file.sh
delete mode 100755 configuration-assistant.perl
create mode 100755 configure
delete mode 100644 debian/patches/build-with-system-libbz2-libz.patch
delete mode 100644 debian/patches/do_not_build_external_libs.patch
delete mode 100644 debian/patches/hardening-format-security.patch
delete mode 100644 doc/help/html/abi-dump-help.html
delete mode 100644 doc/help/html/abi-load-help.html
delete mode 100644 doc/help/html/bam-load-help.html
delete mode 100644 doc/help/html/copycat-help.html
delete mode 100644 doc/help/html/crc32sum-help.html
delete mode 100644 doc/help/html/fastq-dump-help.html
delete mode 100644 doc/help/html/fastq-load-help.html
delete mode 100644 doc/help/html/illumina-dump-help.html
delete mode 100644 doc/help/html/illumina-load-help.html
delete mode 100644 doc/help/html/kar-help.html
delete mode 100644 doc/help/html/kdbmeta-help.html
delete mode 100644 doc/help/html/kqsh-help.html
delete mode 100644 doc/help/html/md5cp-help.html
delete mode 100644 doc/help/html/rcexplain-help.html
delete mode 100644 doc/help/html/sff-dump-help.html
delete mode 100644 doc/help/html/sra-dump-help.html
delete mode 100644 doc/help/html/sra-stat-help.html
delete mode 100644 doc/help/html/srapath-help.html
delete mode 100644 doc/help/html/srf-load-help.html
delete mode 100644 doc/help/html/txt2kdb-help.html
delete mode 100644 doc/help/html/vdb-dump-help.html
delete mode 100644 doc/help/txt/abi-dump-help.txt
delete mode 100644 doc/help/txt/abi-load-help.txt
delete mode 100644 doc/help/txt/bam-loader-help.txt
delete mode 100644 doc/help/txt/copycat-help.txt
delete mode 100644 doc/help/txt/crc32sum-help.txt
delete mode 100644 doc/help/txt/fastq-dump-help.txt
delete mode 100644 doc/help/txt/fastq-load-help.txt
delete mode 100644 doc/help/txt/illumina-dump-help.txt
delete mode 100644 doc/help/txt/illumina-load-help.txt
delete mode 100644 doc/help/txt/kar-help.txt
delete mode 100644 doc/help/txt/kdbmeta-help.txt
delete mode 100644 doc/help/txt/kqsh-help.txt
delete mode 100644 doc/help/txt/md5cp-help.txt
delete mode 100644 doc/help/txt/rcexplain-help.txt
delete mode 100644 doc/help/txt/sff-dump-help.txt
delete mode 100644 doc/help/txt/sra-dump-help.txt
delete mode 100644 doc/help/txt/sra-stat-help.txt
delete mode 100644 doc/help/txt/srapath-help.txt
delete mode 100644 doc/help/txt/srf-load-help.txt
delete mode 100644 doc/help/txt/txt2kdb-help.txt
delete mode 100644 doc/help/txt/vdb-dump-help.txt
delete mode 100644 interfaces/align/align-access.h
delete mode 100644 interfaces/align/align.vschema
delete mode 100644 interfaces/align/alignsrc.h
delete mode 100644 interfaces/align/bam.h
delete mode 100644 interfaces/align/dna-reverse-cmpl.h
delete mode 100644 interfaces/align/extern.h
delete mode 100644 interfaces/align/iterator.h
delete mode 100644 interfaces/align/manager.h
delete mode 100644 interfaces/align/qstat.vschema
delete mode 100644 interfaces/align/quality-quantizer.h
delete mode 100644 interfaces/align/reader-refseq.h
delete mode 100644 interfaces/align/reference.h
delete mode 100644 interfaces/align/refseq-mgr.h
delete mode 100644 interfaces/align/refseq.vschema
delete mode 100644 interfaces/align/seq.vschema
delete mode 100644 interfaces/align/writer-alignment.h
delete mode 100644 interfaces/align/writer-cmn.h
delete mode 100644 interfaces/align/writer-reference.h
delete mode 100644 interfaces/align/writer-refseq.h
delete mode 100644 interfaces/align/writer-sequence.h
delete mode 100644 interfaces/cc/gcc/compiler.h
delete mode 100644 interfaces/cc/gcc/i386/arch-impl.h
delete mode 100644 interfaces/cc/gcc/i386/atomic.h
delete mode 100644 interfaces/cc/gcc/i386/atomic32.h
delete mode 100644 interfaces/cc/gcc/i386/bitstr.h
delete mode 100644 interfaces/cc/gcc/i386/byteswap.h
delete mode 100644 interfaces/cc/gcc/i386/strtol.h
delete mode 100644 interfaces/cc/gcc/noarch/bitstr.h
delete mode 100644 interfaces/cc/gcc/v128.h
delete mode 100644 interfaces/cc/gcc/va_copy.h
delete mode 100644 interfaces/cc/gcc/x86_64/arch-impl.h
delete mode 100644 interfaces/cc/gcc/x86_64/atomic.h
delete mode 100644 interfaces/cc/gcc/x86_64/atomic32.h
delete mode 100644 interfaces/cc/gcc/x86_64/atomic64.h
delete mode 100644 interfaces/cc/gcc/x86_64/bitstr.h
delete mode 100644 interfaces/cc/gcc/x86_64/byteswap.h
delete mode 100644 interfaces/cc/gcc/x86_64/strtol.h
delete mode 100644 interfaces/cc/icc/compiler.h
delete mode 100644 interfaces/cc/vc++/compiler.h
delete mode 100644 interfaces/cc/vc++/i386/arch-impl.h
delete mode 100644 interfaces/cc/vc++/i386/bitstr.h
delete mode 100644 interfaces/cc/vc++/noarch/arch-impl.h
delete mode 100644 interfaces/cc/vc++/noarch/bitstr.h
delete mode 100644 interfaces/cc/vc++/stdbool.h
delete mode 100644 interfaces/cc/vc++/stdint.h
delete mode 100644 interfaces/cc/vc++/va_copy.h
delete mode 100644 interfaces/cc/vc++/x86_64/arch-impl.h
delete mode 100644 interfaces/cc/vc++/x86_64/bitstr.h
delete mode 100644 interfaces/ext/bzlib.h
delete mode 100644 interfaces/ext/libxml/DOCBparser.h
delete mode 100644 interfaces/ext/libxml/HTMLparser.h
delete mode 100644 interfaces/ext/libxml/HTMLtree.h
delete mode 100644 interfaces/ext/libxml/SAX.h
delete mode 100644 interfaces/ext/libxml/SAX2.h
delete mode 100644 interfaces/ext/libxml/c14n.h
delete mode 100644 interfaces/ext/libxml/catalog.h
delete mode 100644 interfaces/ext/libxml/chvalid.h
delete mode 100644 interfaces/ext/libxml/debugXML.h
delete mode 100644 interfaces/ext/libxml/dict.h
delete mode 100644 interfaces/ext/libxml/encoding.h
delete mode 100644 interfaces/ext/libxml/entities.h
delete mode 100644 interfaces/ext/libxml/globals.h
delete mode 100644 interfaces/ext/libxml/hash.h
delete mode 100644 interfaces/ext/libxml/list.h
delete mode 100644 interfaces/ext/libxml/nanoftp.h
delete mode 100644 interfaces/ext/libxml/nanohttp.h
delete mode 100644 interfaces/ext/libxml/parser.h
delete mode 100644 interfaces/ext/libxml/parserInternals.h
delete mode 100644 interfaces/ext/libxml/pattern.h
delete mode 100644 interfaces/ext/libxml/relaxng.h
delete mode 100644 interfaces/ext/libxml/schemasInternals.h
delete mode 100644 interfaces/ext/libxml/schematron.h
delete mode 100644 interfaces/ext/libxml/threads.h
delete mode 100644 interfaces/ext/libxml/tree.h
delete mode 100644 interfaces/ext/libxml/uri.h
delete mode 100644 interfaces/ext/libxml/valid.h
delete mode 100644 interfaces/ext/libxml/xinclude.h
delete mode 100644 interfaces/ext/libxml/xlink.h
delete mode 100644 interfaces/ext/libxml/xmlIO.h
delete mode 100644 interfaces/ext/libxml/xmlautomata.h
delete mode 100644 interfaces/ext/libxml/xmlerror.h
delete mode 100644 interfaces/ext/libxml/xmlexports.h
delete mode 100644 interfaces/ext/libxml/xmlmemory.h
delete mode 100644 interfaces/ext/libxml/xmlmodule.h
delete mode 100644 interfaces/ext/libxml/xmlreader.h
delete mode 100644 interfaces/ext/libxml/xmlregexp.h
delete mode 100644 interfaces/ext/libxml/xmlsave.h
delete mode 100644 interfaces/ext/libxml/xmlschemas.h
delete mode 100644 interfaces/ext/libxml/xmlschemastypes.h
delete mode 100644 interfaces/ext/libxml/xmlstring.h
delete mode 100644 interfaces/ext/libxml/xmlunicode.h
delete mode 100644 interfaces/ext/libxml/xmlversion.h
delete mode 100644 interfaces/ext/libxml/xmlwriter.h
delete mode 100644 interfaces/ext/libxml/xpath.h
delete mode 100644 interfaces/ext/libxml/xpathInternals.h
delete mode 100644 interfaces/ext/libxml/xpointer.h
delete mode 100644 interfaces/ext/magic.h
delete mode 100644 interfaces/ext/regex.h
delete mode 100644 interfaces/ext/zconf.h
delete mode 100644 interfaces/ext/zlib.h
delete mode 100644 interfaces/insdc/insdc.h
delete mode 100644 interfaces/insdc/insdc.vschema
delete mode 100644 interfaces/insdc/seq.vschema
delete mode 100644 interfaces/insdc/sra.h
delete mode 100644 interfaces/insdc/sra.vschema
delete mode 100644 interfaces/kapp/args.h
delete mode 100644 interfaces/kapp/extern.h
delete mode 100644 interfaces/kapp/loader-file.h
delete mode 100644 interfaces/kapp/loader-meta.h
delete mode 100644 interfaces/kapp/log-xml.h
delete mode 100644 interfaces/kapp/main.h
delete mode 100644 interfaces/kapp/progressbar.h
delete mode 100644 interfaces/kapp/queue-file.h
delete mode 100644 interfaces/kdb/btree.h
delete mode 100644 interfaces/kdb/column.h
delete mode 100644 interfaces/kdb/consistency-check.h
delete mode 100644 interfaces/kdb/database.h
delete mode 100644 interfaces/kdb/extern.h
delete mode 100644 interfaces/kdb/index.h
delete mode 100644 interfaces/kdb/kdb-priv.h
delete mode 100644 interfaces/kdb/manager.h
delete mode 100644 interfaces/kdb/meta.h
delete mode 100644 interfaces/kdb/meta.hpp
delete mode 100644 interfaces/kdb/namelist.h
delete mode 100644 interfaces/kdb/table.h
delete mode 100644 interfaces/kfc/callconv.h
delete mode 100644 interfaces/kfc/ctx.h
delete mode 100644 interfaces/kfc/defs.h
delete mode 100644 interfaces/kfc/except.h
delete mode 100644 interfaces/kfc/extern.h
delete mode 100644 interfaces/kfc/rc.h
delete mode 100644 interfaces/kfc/rsrc.h
delete mode 100644 interfaces/kfc/xc.h
delete mode 100644 interfaces/kfc/xcdefs.h
delete mode 100644 interfaces/kfc/xcext.h
delete mode 100644 interfaces/kfc/xcgen.h
delete mode 100644 interfaces/kfg/config.h
delete mode 100644 interfaces/kfg/extern.h
delete mode 100644 interfaces/kfg/kart.h
delete mode 100644 interfaces/kfg/keystore-priv.h
delete mode 100644 interfaces/kfg/keystore.h
delete mode 100644 interfaces/kfg/kfg-priv.h
delete mode 100644 interfaces/kfg/repository.h
delete mode 100644 interfaces/kfs/arc.h
delete mode 100644 interfaces/kfs/arrayfile.h
delete mode 100644 interfaces/kfs/buffile.h
delete mode 100644 interfaces/kfs/bzip.h
delete mode 100644 interfaces/kfs/cacheteefile.h
delete mode 100644 interfaces/kfs/countfile.h
delete mode 100644 interfaces/kfs/crc.h
delete mode 100644 interfaces/kfs/defs.h
delete mode 100644 interfaces/kfs/directory.h
delete mode 100644 interfaces/kfs/directory.hpp
delete mode 100644 interfaces/kfs/dyload.h
delete mode 100644 interfaces/kfs/extern.h
delete mode 100644 interfaces/kfs/ffext.h
delete mode 100644 interfaces/kfs/ffmagic.h
delete mode 100644 interfaces/kfs/file.h
delete mode 100644 interfaces/kfs/file.hpp
delete mode 100644 interfaces/kfs/fileformat.h
delete mode 100644 interfaces/kfs/gzip.h
delete mode 100644 interfaces/kfs/impl.h
delete mode 100644 interfaces/kfs/kfs-priv.h
delete mode 100644 interfaces/kfs/lockfile.h
delete mode 100644 interfaces/kfs/md5.h
delete mode 100644 interfaces/kfs/mmap.h
delete mode 100644 interfaces/kfs/nullfile.h
delete mode 100644 interfaces/kfs/pagefile.h
delete mode 100644 interfaces/kfs/pmem.h
delete mode 100644 interfaces/kfs/quickmount.h
delete mode 100644 interfaces/kfs/ramfile.h
delete mode 100644 interfaces/kfs/readheadfile.h
delete mode 100644 interfaces/kfs/sra.h
delete mode 100644 interfaces/kfs/subfile.h
delete mode 100644 interfaces/kfs/tar.h
delete mode 100644 interfaces/kfs/teefile.h
delete mode 100644 interfaces/kfs/toc.h
delete mode 100644 interfaces/klib/callconv.h
delete mode 100644 interfaces/klib/checksum.h
delete mode 100644 interfaces/klib/container.h
delete mode 100644 interfaces/klib/data-buffer.h
delete mode 100644 interfaces/klib/debug.h
delete mode 100644 interfaces/klib/defs.h
delete mode 100644 interfaces/klib/extern.h
delete mode 100644 interfaces/klib/impl.h
delete mode 100644 interfaces/klib/klib-priv.h
delete mode 100644 interfaces/klib/ksort-macro.h
delete mode 100644 interfaces/klib/log.h
delete mode 100644 interfaces/klib/logfmt.h
delete mode 100644 interfaces/klib/misc.h
delete mode 100644 interfaces/klib/namelist.h
delete mode 100644 interfaces/klib/namelist.hpp
delete mode 100644 interfaces/klib/out.h
delete mode 100644 interfaces/klib/pack.h
delete mode 100644 interfaces/klib/pbstree.h
delete mode 100644 interfaces/klib/printf.h
delete mode 100644 interfaces/klib/ptrie.h
delete mode 100644 interfaces/klib/rc.h
delete mode 100644 interfaces/klib/refcount.h
delete mode 100644 interfaces/klib/report.h
delete mode 100644 interfaces/klib/sort.h
delete mode 100644 interfaces/klib/sra-release-version.h
delete mode 100644 interfaces/klib/status.h
delete mode 100644 interfaces/klib/symbol.h
delete mode 100644 interfaces/klib/symtab.h
delete mode 100644 interfaces/klib/text.h
delete mode 100644 interfaces/klib/time.h
delete mode 100644 interfaces/klib/token.h
delete mode 100644 interfaces/klib/trie.h
delete mode 100644 interfaces/klib/vector.h
delete mode 100644 interfaces/klib/vlen-encode.h
delete mode 100644 interfaces/klib/writer.h
delete mode 100644 interfaces/kns/adapt.h
delete mode 100644 interfaces/kns/ascp.h
delete mode 100644 interfaces/kns/endpoint.h
delete mode 100644 interfaces/kns/extern.h
delete mode 100644 interfaces/kns/http.h
delete mode 100644 interfaces/kns/impl.h
delete mode 100644 interfaces/kns/manager-ext.h
delete mode 100644 interfaces/kns/manager.h
delete mode 100644 interfaces/kns/socket.h
delete mode 100644 interfaces/kns/stream.h
delete mode 100644 interfaces/kproc/barrier.h
delete mode 100644 interfaces/kproc/barrier.hpp
delete mode 100644 interfaces/kproc/cond.h
delete mode 100644 interfaces/kproc/cond.hpp
delete mode 100644 interfaces/kproc/extern.h
delete mode 100644 interfaces/kproc/impl.h
delete mode 100644 interfaces/kproc/lock.h
delete mode 100644 interfaces/kproc/lock.hpp
delete mode 100644 interfaces/kproc/procmgr.h
delete mode 100644 interfaces/kproc/q-extern.h
delete mode 100644 interfaces/kproc/queue.h
delete mode 100644 interfaces/kproc/sem.h
delete mode 100644 interfaces/kproc/sem.hpp
delete mode 100644 interfaces/kproc/task.h
delete mode 100644 interfaces/kproc/thread.h
delete mode 100644 interfaces/kproc/thread.hpp
delete mode 100644 interfaces/kproc/timeout.h
delete mode 100644 interfaces/krypto/cipher-impl.h
delete mode 100644 interfaces/krypto/cipher-priv.h
delete mode 100644 interfaces/krypto/cipher-test.h
delete mode 100644 interfaces/krypto/cipher.h
delete mode 100644 interfaces/krypto/ciphermgr-priv.h
delete mode 100644 interfaces/krypto/ciphermgr.h
delete mode 100644 interfaces/krypto/encfile-priv.h
delete mode 100644 interfaces/krypto/encfile.h
delete mode 100644 interfaces/krypto/extern.h
delete mode 100644 interfaces/krypto/key.h
delete mode 100644 interfaces/krypto/manager-priv.h
delete mode 100644 interfaces/krypto/manager.h
delete mode 100644 interfaces/krypto/reencfile.h
delete mode 100644 interfaces/krypto/rng-impl.h
delete mode 100644 interfaces/krypto/rng.h
delete mode 100644 interfaces/krypto/testciphermgr.h
delete mode 100644 interfaces/krypto/wgaencrypt.h
delete mode 100644 interfaces/ktst/test_tools.hpp
delete mode 100644 interfaces/ktst/unit_test.hpp
delete mode 100644 interfaces/ktst/unit_test_suite.hpp
delete mode 100644 interfaces/kxml/xml.h
delete mode 100644 interfaces/loader/alignment-writer.h
delete mode 100644 interfaces/loader/common-reader-priv.h
delete mode 100644 interfaces/loader/common-reader.h
delete mode 100644 interfaces/loader/common-writer.h
delete mode 100644 interfaces/loader/mmarray.h
delete mode 100644 interfaces/loader/reference-writer.h
delete mode 100644 interfaces/loader/sequence-writer.h
delete mode 100644 interfaces/ncbi/clip.vschema
delete mode 100644 interfaces/ncbi/extern.h
delete mode 100644 interfaces/ncbi/ncbi.vschema
delete mode 100644 interfaces/ncbi/seq.vschema
delete mode 100644 interfaces/ncbi/spotname.vschema
delete mode 100644 interfaces/ncbi/sra.vschema
delete mode 100644 interfaces/ncbi/stats.vschema
delete mode 100644 interfaces/ncbi/vdb-blast-priv.h
delete mode 100644 interfaces/ncbi/vdb-blast.h
delete mode 100644 interfaces/ncbi/wgs-contig.h
delete mode 100644 interfaces/ncbi/wgs-contig.vschema
delete mode 100644 interfaces/os/linux/os-native.h
delete mode 100644 interfaces/os/mac/byteswap.h
delete mode 100644 interfaces/os/mac/endian.h
delete mode 100644 interfaces/os/mac/os-native.h
delete mode 100644 interfaces/os/unix/sysalloc.h
delete mode 100644 interfaces/os/unix/unix-native.h
delete mode 100644 interfaces/os/win/atomic.h
delete mode 100644 interfaces/os/win/atomic32.h
delete mode 100644 interfaces/os/win/atomic64.h
delete mode 100644 interfaces/os/win/byteswap.h
delete mode 100644 interfaces/os/win/endian.h
delete mode 100644 interfaces/os/win/os-native.h
delete mode 100644 interfaces/os/win/strtol.h
delete mode 100644 interfaces/os/win/sysalloc.h
delete mode 100644 interfaces/search/extern.h
delete mode 100644 interfaces/search/grep.h
delete mode 100644 interfaces/search/nucstrstr.h
delete mode 100644 interfaces/sra/454.vschema
delete mode 100644 interfaces/sra/abi.h
delete mode 100644 interfaces/sra/abi.vschema
delete mode 100644 interfaces/sra/extern.h
delete mode 100644 interfaces/sra/fastq.h
delete mode 100644 interfaces/sra/helicos.vschema
delete mode 100644 interfaces/sra/illumina.h
delete mode 100644 interfaces/sra/illumina.vschema
delete mode 100644 interfaces/sra/impl.h
delete mode 100644 interfaces/sra/ion-torrent.vschema
delete mode 100644 interfaces/sra/pacbio.h
delete mode 100644 interfaces/sra/path-extern.h
delete mode 100644 interfaces/sra/pevents.vschema
delete mode 100644 interfaces/sra/rd-extern.h
delete mode 100644 interfaces/sra/sch-extern.h
delete mode 100644 interfaces/sra/sff-file.h
delete mode 100644 interfaces/sra/sff.h
delete mode 100644 interfaces/sra/sradb-priv.h
delete mode 100644 interfaces/sra/sradb.h
delete mode 100644 interfaces/sra/sradb.hpp
delete mode 100644 interfaces/sra/srapath.h
delete mode 100644 interfaces/sra/srapath.hpp
delete mode 100644 interfaces/sra/sraschema.h
delete mode 100644 interfaces/sra/types.h
delete mode 100644 interfaces/sra/wsradb.h
delete mode 100644 interfaces/sra/wsradb.hpp
delete mode 100644 interfaces/vdb/blob.h
delete mode 100644 interfaces/vdb/built-in.vschema
delete mode 100644 interfaces/vdb/cursor.h
delete mode 100644 interfaces/vdb/cursor.hpp
delete mode 100644 interfaces/vdb/database.h
delete mode 100644 interfaces/vdb/dependencies.h
delete mode 100644 interfaces/vdb/extern.h
delete mode 100644 interfaces/vdb/manager.h
delete mode 100644 interfaces/vdb/manager.hpp
delete mode 100644 interfaces/vdb/report.h
delete mode 100644 interfaces/vdb/schema.h
delete mode 100644 interfaces/vdb/table.h
delete mode 100644 interfaces/vdb/table.hpp
delete mode 100644 interfaces/vdb/types.h
delete mode 100644 interfaces/vdb/types.hpp
delete mode 100644 interfaces/vdb/vdb-priv.h
delete mode 100644 interfaces/vdb/vdb.vschema
delete mode 100644 interfaces/vdb/xform.h
delete mode 100644 interfaces/vfs/extern.h
delete mode 100644 interfaces/vfs/manager-priv.h
delete mode 100644 interfaces/vfs/manager.h
delete mode 100644 interfaces/vfs/path-priv.h
delete mode 100644 interfaces/vfs/path.h
delete mode 100644 interfaces/vfs/resolver.h
create mode 100644 konfigure.perl
delete mode 100644 libs/Makefile
delete mode 100644 libs/align/Makefile
delete mode 100644 libs/align/al_iterator.c
delete mode 100644 libs/align/align-access.c
delete mode 100644 libs/align/align_mgr.c
delete mode 100644 libs/align/bam-priv.h
delete mode 100644 libs/align/bam.c
delete mode 100644 libs/align/debug.h
delete mode 100644 libs/align/dna-reverse-cmpl.c
delete mode 100644 libs/align/pl_iterator.c
delete mode 100644 libs/align/quality-quantizer.c
delete mode 100644 libs/align/reader-cmn.c
delete mode 100644 libs/align/reader-cmn.h
delete mode 100644 libs/align/reader-refseq.c
delete mode 100644 libs/align/ref_iterator.c
delete mode 100644 libs/align/reference-cmn.c
delete mode 100644 libs/align/reference-cmn.h
delete mode 100644 libs/align/reference.c
delete mode 100644 libs/align/refseq-mgr-priv.h
delete mode 100644 libs/align/refseq-mgr.c
delete mode 100644 libs/align/writer-alignment.c
delete mode 100644 libs/align/writer-cmn.c
delete mode 100644 libs/align/writer-priv.h
delete mode 100644 libs/align/writer-ref.c
delete mode 100644 libs/align/writer-ref.h
delete mode 100644 libs/align/writer-reference.c
delete mode 100644 libs/align/writer-refseq.c
delete mode 100644 libs/align/writer-sequence.c
delete mode 100644 libs/ascp/Makefile
delete mode 100644 libs/ascp/ascp-priv.h
delete mode 100644 libs/ascp/ascp.c
delete mode 100644 libs/ascp/linux/ascp-path.c
delete mode 100644 libs/ascp/mac/ascp-path.c
delete mode 100644 libs/ascp/unix/connect.c
delete mode 100644 libs/ascp/win/ascp-path.c
delete mode 100644 libs/ascp/win/connect.c
delete mode 100644 libs/axf/Makefile
delete mode 100644 libs/axf/align-local_ref_id.c
delete mode 100644 libs/axf/align-local_ref_start.c
delete mode 100644 libs/axf/align-ref-name.c
delete mode 100644 libs/axf/align-ref-pos.c
delete mode 100644 libs/axf/align-ref-seq-id.c
delete mode 100644 libs/axf/align-restore-read.c
delete mode 100644 libs/axf/cigar.c
delete mode 100644 libs/axf/generate-mismatch-qual.c
delete mode 100644 libs/axf/get-sam-flags.c
delete mode 100644 libs/axf/get_mate_align_ids.c
delete mode 100644 libs/axf/make-cmp-read_desc.c
delete mode 100644 libs/axf/mismatch-restore-qual.c
delete mode 100644 libs/axf/not-my-row.c
delete mode 100644 libs/axf/project_read_from_sequence.c
delete mode 100644 libs/axf/raw-restore-qual.c
delete mode 100644 libs/axf/raw-restore-read.c
delete mode 100644 libs/axf/ref-preserve_qual.c
delete mode 100644 libs/axf/ref-restore-read.c
delete mode 100644 libs/axf/ref-tbl-sub-select.c
delete mode 100644 libs/axf/ref-tbl.c
delete mode 100644 libs/axf/ref-tbl.h
delete mode 100644 libs/axf/refseq-stats.c
delete mode 100644 libs/axf/seq-construct-read.c
delete mode 100644 libs/axf/seq-restore-read.c
delete mode 100644 libs/axf/template-len.c
delete mode 100644 libs/blast/Makefile
delete mode 100644 libs/blast/blast.c
delete mode 100644 libs/kapp/Makefile
delete mode 100644 libs/kapp/args.c
delete mode 100644 libs/kapp/args_debug.h
delete mode 100644 libs/kapp/loader-file.c
delete mode 100644 libs/kapp/loader-meta.c
delete mode 100644 libs/kapp/log-xml.c
delete mode 100644 libs/kapp/main-priv.h
delete mode 100644 libs/kapp/main.c
delete mode 100644 libs/kapp/progressbar.c
delete mode 100644 libs/kapp/queue-file.c
delete mode 100644 libs/kapp/tokenizer.c
delete mode 100644 libs/kapp/unix/sysmain.c
delete mode 100644 libs/kapp/win/sysmain.c
delete mode 100644 libs/kdb/Makefile
delete mode 100644 libs/kdb/btree.c
delete mode 100644 libs/kdb/cc-priv.h
delete mode 100644 libs/kdb/coldata-priv.h
delete mode 100644 libs/kdb/coldata.c
delete mode 100644 libs/kdb/colfmt-priv.h
delete mode 100644 libs/kdb/colidx-priv.h
delete mode 100644 libs/kdb/colidx.c
delete mode 100644 libs/kdb/colidx0-priv.h
delete mode 100644 libs/kdb/colidx0.c
delete mode 100644 libs/kdb/colidx1-priv.h
delete mode 100644 libs/kdb/colidx1.c
delete mode 100644 libs/kdb/colidx2-priv.h
delete mode 100644 libs/kdb/colidx2.c
delete mode 100644 libs/kdb/column-cc.c
delete mode 100644 libs/kdb/column-priv.h
delete mode 100644 libs/kdb/column.c
delete mode 100644 libs/kdb/database-cc.c
delete mode 100644 libs/kdb/database-cmn.c
delete mode 100644 libs/kdb/database-priv.h
delete mode 100644 libs/kdb/database.c
delete mode 100644 libs/kdb/dbcc-cmn.c
delete mode 100644 libs/kdb/dbmgr-cmn.c
delete mode 100644 libs/kdb/dbmgr-priv.h
delete mode 100644 libs/kdb/dbmgr.c
delete mode 100644 libs/kdb/idstats-priv.h
delete mode 100644 libs/kdb/idstats.c
delete mode 100644 libs/kdb/idxblk-priv.h
delete mode 100644 libs/kdb/idxblk.c
delete mode 100644 libs/kdb/index-cmn.h
delete mode 100644 libs/kdb/index-priv.h
delete mode 100644 libs/kdb/index.c
delete mode 100644 libs/kdb/kdb-priv.h
delete mode 100644 libs/kdb/kdb.c
delete mode 100644 libs/kdb/kdbfmt-priv.h
delete mode 100644 libs/kdb/libkdb.vers.h
delete mode 100644 libs/kdb/libwkdb.vers.h
delete mode 100644 libs/kdb/meta.c
delete mode 100644 libs/kdb/ptrieval-v1.c
delete mode 100644 libs/kdb/ptrieval-v2.c
delete mode 100644 libs/kdb/table-cc.c
delete mode 100644 libs/kdb/table-priv.h
delete mode 100644 libs/kdb/table.c
delete mode 100644 libs/kdb/trieidx-priv.h
delete mode 100644 libs/kdb/trieidx-v1.c
delete mode 100644 libs/kdb/trieidx-v2.c
delete mode 100644 libs/kdb/trieval-v1.c
delete mode 100644 libs/kdb/trieval-v2.c
delete mode 100644 libs/kdb/u64idx-v3.c
delete mode 100644 libs/kdb/wcoldata-priv.h
delete mode 100644 libs/kdb/wcoldata.c
delete mode 100644 libs/kdb/wcolidx-priv.h
delete mode 100644 libs/kdb/wcolidx.c
delete mode 100644 libs/kdb/wcolidx0-priv.h
delete mode 100644 libs/kdb/wcolidx0.c
delete mode 100644 libs/kdb/wcolidx1-priv.h
delete mode 100644 libs/kdb/wcolidx1.c
delete mode 100644 libs/kdb/wcolidx2-priv.h
delete mode 100644 libs/kdb/wcolidx2.c
delete mode 100644 libs/kdb/wcolumn-priv.h
delete mode 100644 libs/kdb/wcolumn.c
delete mode 100644 libs/kdb/wdatabase-priv.h
delete mode 100644 libs/kdb/wdatabase.c
delete mode 100644 libs/kdb/wdbmgr.c
delete mode 100644 libs/kdb/werror-priv.h
delete mode 100644 libs/kdb/widxblk-priv.h
delete mode 100644 libs/kdb/widxblk.c
delete mode 100644 libs/kdb/windex-priv.h
delete mode 100644 libs/kdb/windex.c
delete mode 100644 libs/kdb/wkdb-priv.h
delete mode 100644 libs/kdb/wkdb.c
delete mode 100644 libs/kdb/wmeta.c
delete mode 100644 libs/kdb/wtable-priv.h
delete mode 100644 libs/kdb/wtable.c
delete mode 100644 libs/kdb/wtrieidx-v1.c
delete mode 100644 libs/kdb/wtrieidx-v2.c
delete mode 100644 libs/kdb/wu64idx-v3.c
delete mode 100644 libs/kfg/Makefile
delete mode 100644 libs/kfg/config-grammar.c
delete mode 100644 libs/kfg/config-lex.c
delete mode 100644 libs/kfg/config-tokens.h
delete mode 100644 libs/kfg/config.c
delete mode 100644 libs/kfg/default.kfg
delete mode 100644 libs/kfg/kart.c
delete mode 100644 libs/kfg/keystore.c
delete mode 100644 libs/kfg/kfg-parse.h
delete mode 100644 libs/kfg/report-kfg.c
delete mode 100644 libs/kfg/repository.c
delete mode 100644 libs/kfs/Makefile
delete mode 100644 libs/kfs/arc.c
delete mode 100644 libs/kfs/arrayfile.c
delete mode 100644 libs/kfs/buffile-read.c
delete mode 100644 libs/kfs/buffile-write.c
delete mode 100644 libs/kfs/buffile.c
delete mode 100644 libs/kfs/bzip.c
delete mode 100644 libs/kfs/cacheteefile.c
delete mode 100644 libs/kfs/countfile.c
delete mode 100644 libs/kfs/crc32.c
delete mode 100644 libs/kfs/dir_test.c
delete mode 100644 libs/kfs/directory.c
delete mode 100644 libs/kfs/ffext.c
delete mode 100644 libs/kfs/ffkey.c
delete mode 100644 libs/kfs/ffmagic.c
delete mode 100644 libs/kfs/file.c
delete mode 100644 libs/kfs/fileformat-priv.h
delete mode 100644 libs/kfs/fileformat.c
delete mode 100644 libs/kfs/from_to_namelist.c
delete mode 100644 libs/kfs/gzip.c
delete mode 100644 libs/kfs/impl.h
delete mode 100644 libs/kfs/karc-priv.h
delete mode 100644 libs/kfs/kfs-priv.h
delete mode 100644 libs/kfs/lockfile.c
delete mode 100644 libs/kfs/md5.c
delete mode 100644 libs/kfs/mmap-priv.h
delete mode 100644 libs/kfs/mmap.c
delete mode 100644 libs/kfs/nullfile.c
delete mode 100644 libs/kfs/pagefile.c
delete mode 100644 libs/kfs/pmem.c
delete mode 100644 libs/kfs/quickmount.c
delete mode 100644 libs/kfs/ramfile.c
delete mode 100644 libs/kfs/readheadfile.c
delete mode 100644 libs/kfs/report.c
delete mode 100644 libs/kfs/sra.c
delete mode 100644 libs/kfs/subfile.c
delete mode 100644 libs/kfs/tar.c
delete mode 100644 libs/kfs/teefile.c
delete mode 100644 libs/kfs/toc-priv.h
delete mode 100644 libs/kfs/toc.c
delete mode 100644 libs/kfs/tocdir.c
delete mode 100644 libs/kfs/tocentry.c
delete mode 100644 libs/kfs/tocfile.c
delete mode 100644 libs/kfs/unix/sysdir-priv.h
delete mode 100644 libs/kfs/unix/sysdir.c
delete mode 100644 libs/kfs/unix/sysdll.c
delete mode 100644 libs/kfs/unix/sysfile-priv.h
delete mode 100644 libs/kfs/unix/sysfile.c
delete mode 100644 libs/kfs/unix/syslockfile.c
delete mode 100644 libs/kfs/unix/sysmmap-priv.h
delete mode 100644 libs/kfs/unix/sysmmap.c
delete mode 100644 libs/kfs/win/lnk_tools.c
delete mode 100644 libs/kfs/win/sysdir-priv.h
delete mode 100644 libs/kfs/win/sysdir.c
delete mode 100644 libs/kfs/win/sysdll.c
delete mode 100644 libs/kfs/win/sysfile-priv.h
delete mode 100644 libs/kfs/win/sysfile.c
delete mode 100644 libs/kfs/win/syslockfile.c
delete mode 100644 libs/kfs/win/sysmmap-priv.h
delete mode 100644 libs/kfs/win/sysmmap.c
delete mode 100644 libs/klib/Judy.h
delete mode 100644 libs/klib/Makefile
delete mode 100644 libs/klib/SHA-32bit.c
delete mode 100644 libs/klib/SHA-64bit.c
delete mode 100644 libs/klib/bsearch.c
delete mode 100644 libs/klib/bstpersist.c
delete mode 100644 libs/klib/container.c
delete mode 100644 libs/klib/cp1252.c
delete mode 100644 libs/klib/crc32.c
delete mode 100644 libs/klib/data-buffer.c
delete mode 100644 libs/klib/debug.c
delete mode 100644 libs/klib/iso8859-1.c
delete mode 100644 libs/klib/iso8859.c
delete mode 100644 libs/klib/judy-vector.c
delete mode 100644 libs/klib/judy/Judy1.h
delete mode 100644 libs/klib/judy/JudyByCount.c
delete mode 100644 libs/klib/judy/JudyByCountWithDefs.c
delete mode 100644 libs/klib/judy/JudyCascade.c
delete mode 100644 libs/klib/judy/JudyCount.c
delete mode 100644 libs/klib/judy/JudyCreateBranch.c
delete mode 100644 libs/klib/judy/JudyDecascade.c
delete mode 100644 libs/klib/judy/JudyDel.c
delete mode 100644 libs/klib/judy/JudyFirst.c
delete mode 100644 libs/klib/judy/JudyFreeArray.c
delete mode 100644 libs/klib/judy/JudyGet.c
delete mode 100644 libs/klib/judy/JudyHS.c
delete mode 100644 libs/klib/judy/JudyHS.h
delete mode 100644 libs/klib/judy/JudyIns.c
delete mode 100644 libs/klib/judy/JudyInsArray.c
delete mode 100644 libs/klib/judy/JudyInsertBranch.c
delete mode 100644 libs/klib/judy/JudyL.h
delete mode 100644 libs/klib/judy/JudyMalloc.c
delete mode 100644 libs/klib/judy/JudyMallocIF.c
delete mode 100644 libs/klib/judy/JudyMemActive.c
delete mode 100644 libs/klib/judy/JudyMemUsed.c
delete mode 100644 libs/klib/judy/JudyNext.c
delete mode 100644 libs/klib/judy/JudyNextEmpty.c
delete mode 100644 libs/klib/judy/JudyPrev.c
delete mode 100644 libs/klib/judy/JudyPrevEmpty.c
delete mode 100644 libs/klib/judy/JudyPrevNext.c
delete mode 100644 libs/klib/judy/JudyPrevNextEmpty.c
delete mode 100644 libs/klib/judy/JudyPrintJP.c
delete mode 100644 libs/klib/judy/JudyPrivate.h
delete mode 100644 libs/klib/judy/JudyPrivate1L.h
delete mode 100644 libs/klib/judy/JudyPrivateBranch.h
delete mode 100644 libs/klib/judy/JudySL.c
delete mode 100644 libs/klib/judy/JudyTablesGen.c
delete mode 100644 libs/klib/judy/Makefile
delete mode 100644 libs/klib/judy/j__udyGet.c
delete mode 100644 libs/klib/ksort.c
delete mode 100644 libs/klib/log-priv.h
delete mode 100644 libs/klib/log.c
delete mode 100644 libs/klib/maybeswap.h
delete mode 100644 libs/klib/md5.c
delete mode 100644 libs/klib/namelist.c
delete mode 100644 libs/klib/out.c
delete mode 100644 libs/klib/pack.c
delete mode 100644 libs/klib/pbstree-impl.c
delete mode 100644 libs/klib/pbstree-native.c
delete mode 100644 libs/klib/pbstree-priv.h
delete mode 100644 libs/klib/pbstree-swapped.c
delete mode 100644 libs/klib/pbstree.c
delete mode 100644 libs/klib/printf.c
delete mode 100644 libs/klib/ptpersist.c
delete mode 100644 libs/klib/ptrie.c
delete mode 100644 libs/klib/qsort.c
delete mode 100644 libs/klib/rc-idx-tbl.c
delete mode 100644 libs/klib/rc-tbl.c
delete mode 100644 libs/klib/refcount.c
delete mode 100644 libs/klib/release-vers.h
delete mode 100644 libs/klib/report.c
delete mode 100644 libs/klib/sra-release-version.c
delete mode 100644 libs/klib/status-rc-strings.c
delete mode 100644 libs/klib/status-rc.c
delete mode 100644 libs/klib/status.c
delete mode 100644 libs/klib/symtab.c
delete mode 100644 libs/klib/text.c
delete mode 100644 libs/klib/token.c
delete mode 100644 libs/klib/trie-priv.h
delete mode 100644 libs/klib/trie.c
delete mode 100644 libs/klib/trieval.c
delete mode 100644 libs/klib/unix/misc.c
delete mode 100644 libs/klib/unix/syserrcode.c
delete mode 100644 libs/klib/unix/syslog.c
delete mode 100644 libs/klib/unix/systime.c
delete mode 100644 libs/klib/unix/syswriter.c
delete mode 100644 libs/klib/unpack.c
delete mode 100644 libs/klib/utf8.c
delete mode 100644 libs/klib/vector.c
delete mode 100644 libs/klib/vector_namelist.c
delete mode 100644 libs/klib/vlen-encode.c
delete mode 100644 libs/klib/win/misc.c
delete mode 100644 libs/klib/win/sysalloc.c
delete mode 100644 libs/klib/win/syserrcode.c
delete mode 100644 libs/klib/win/syslog.c
delete mode 100644 libs/klib/win/systime.c
delete mode 100644 libs/klib/win/syswriter.c
delete mode 100644 libs/klib/writer-priv.h
delete mode 100644 libs/klib/writer.c
delete mode 100644 libs/kns/Makefile
delete mode 100644 libs/kns/endpoint.c
delete mode 100644 libs/kns/http-priv.h
delete mode 100644 libs/kns/http-test.c
delete mode 100644 libs/kns/http.c
delete mode 100644 libs/kns/kns_manager-ext.c
delete mode 100644 libs/kns/kns_manager.c
delete mode 100644 libs/kns/linux/sysendpoint.c
delete mode 100644 libs/kns/linux/syspoll.c
delete mode 100644 libs/kns/mac/sysendpoint.c
delete mode 100644 libs/kns/mac/syspoll.c
delete mode 100644 libs/kns/manager.c
delete mode 100644 libs/kns/mgr-priv.h
delete mode 100644 libs/kns/poll-priv.h
delete mode 100644 libs/kns/stream-from-files.c
delete mode 100644 libs/kns/stream-from-streams.c
delete mode 100644 libs/kns/stream-priv.h
delete mode 100644 libs/kns/stream.c
delete mode 100644 libs/kns/sysmgr.h
delete mode 100644 libs/kns/undyinghttp.c
delete mode 100644 libs/kns/unix/sysmgr.c
delete mode 100644 libs/kns/unix/syssock.c
delete mode 100644 libs/kns/unix/sysstream.c
delete mode 100644 libs/kns/url-fetcher-curl.c
delete mode 100644 libs/kns/url-fetcher-impl.h
delete mode 100644 libs/kns/url-fetcher.c
delete mode 100644 libs/kns/win/sysendpoint.c
delete mode 100644 libs/kns/win/sysmgr.c
delete mode 100644 libs/kns/win/syssock.c
delete mode 100644 libs/kns/win/sysstream.c
delete mode 100644 libs/kproc/Makefile
delete mode 100644 libs/kproc/bsd/syslock-priv.h
delete mode 100644 libs/kproc/bsd/syslock.c
delete mode 100644 libs/kproc/linux/sysbarrier.c
delete mode 100644 libs/kproc/linux/syslock-priv.h
delete mode 100644 libs/kproc/linux/syslock.c
delete mode 100644 libs/kproc/procmgr.c
delete mode 100644 libs/kproc/queue.c
delete mode 100644 libs/kproc/sem.c
delete mode 100644 libs/kproc/stbarrier.c
delete mode 100644 libs/kproc/stcond.c
delete mode 100644 libs/kproc/stlock.c
delete mode 100644 libs/kproc/stsem.c
delete mode 100644 libs/kproc/stthread.c
delete mode 100644 libs/kproc/sttimeout.c
delete mode 100644 libs/kproc/task.c
delete mode 100644 libs/kproc/unix/syscond-priv.h
delete mode 100644 libs/kproc/unix/syscond.c
delete mode 100644 libs/kproc/unix/systhread.c
delete mode 100644 libs/kproc/unix/systimeout.c
delete mode 100644 libs/kproc/win/syscond-priv.h
delete mode 100644 libs/kproc/win/syscond.c
delete mode 100644 libs/kproc/win/syslock-priv.h
delete mode 100644 libs/kproc/win/syslock.c
delete mode 100644 libs/krypto/Makefile
delete mode 100644 libs/krypto/aes-byte.c
delete mode 100644 libs/krypto/aes-ncbi-priv.h
delete mode 100644 libs/krypto/aes-ncbi.c
delete mode 100644 libs/krypto/aes-priv.h
delete mode 100644 libs/krypto/aes.c
delete mode 100644 libs/krypto/aes_core.c
delete mode 100644 libs/krypto/blockcipher-impl.h
delete mode 100644 libs/krypto/blockcipher-priv.h
delete mode 100644 libs/krypto/blockcipher.c
delete mode 100644 libs/krypto/cipher-byte.c
delete mode 100644 libs/krypto/cipher-impl.h
delete mode 100644 libs/krypto/cipher-no-vec.c
delete mode 100644 libs/krypto/cipher-priv.h
delete mode 100644 libs/krypto/cipher-vec.c
delete mode 100644 libs/krypto/cipher.c
delete mode 100644 libs/krypto/ciphermgr.c
delete mode 100644 libs/krypto/compile-test.c
delete mode 100644 libs/krypto/csprng.c
delete mode 100644 libs/krypto/encfile-priv.h
delete mode 100644 libs/krypto/encfile.c
delete mode 100644 libs/krypto/encfilev2.c
delete mode 100644 libs/krypto/key.c
delete mode 100644 libs/krypto/manager.c
delete mode 100644 libs/krypto/ncbi-priv.h
delete mode 100644 libs/krypto/no-null-ncbi.c
delete mode 100644 libs/krypto/null-ncbi-priv.h
delete mode 100644 libs/krypto/null-ncbi.c
delete mode 100644 libs/krypto/reencfile.c
delete mode 100644 libs/krypto/rng-impl.h
delete mode 100644 libs/krypto/rng-priv.h
delete mode 100644 libs/krypto/rng.c
delete mode 100644 libs/krypto/testcipher.c
delete mode 100644 libs/krypto/wgaencrypt.c
delete mode 100644 libs/ktst/Makefile
delete mode 100644 libs/ktst/testcase.cpp
delete mode 100644 libs/ktst/testenv.cpp
delete mode 100644 libs/ktst/testrunner.cpp
delete mode 100644 libs/ktst/unix/runprocesstestcase.cpp
delete mode 100644 libs/ktst/win/runprocesstestcase.cpp
delete mode 100644 libs/kxml/Makefile
delete mode 100644 libs/kxml/xml.c
delete mode 100644 libs/kxml/xtoc-parsexml.c
delete mode 100644 libs/kxml/xtoc-priv.h
delete mode 100644 libs/kxml/xtoc.c
delete mode 100644 libs/loader/Makefile
delete mode 100644 libs/loader/alignment-writer.c
delete mode 100644 libs/loader/common-reader.c
delete mode 100644 libs/loader/common-writer.c
delete mode 100644 libs/loader/mmarray.c
delete mode 100644 libs/loader/reference-writer.c
delete mode 100644 libs/loader/sequence-writer.c
delete mode 100644 libs/ncbi-vdb/Makefile
delete mode 100644 libs/ncbi-vdb/libncbi-vdb.vers
delete mode 100644 libs/ncbi-vdb/libncbi-wvdb.vers
delete mode 100644 libs/search/Makefile
delete mode 100644 libs/search/agrep-dp.c
delete mode 100644 libs/search/agrep-myers.c
delete mode 100644 libs/search/agrep-myersunltd.c
delete mode 100644 libs/search/agrep-wumanber.c
delete mode 100644 libs/search/debug.h
delete mode 100644 libs/search/fgrep-aho.c
delete mode 100644 libs/search/fgrep-boyermoore.c
delete mode 100644 libs/search/fgrep-dumb.c
delete mode 100644 libs/search/nucstrstr-icc-i386-dbg.pic.s
delete mode 100644 libs/search/nucstrstr-icc-i386-prof.pic.s
delete mode 100644 libs/search/nucstrstr-icc-i386-rel.pic.s
delete mode 100644 libs/search/nucstrstr-icc-x86_64-dbg.pic.s
delete mode 100644 libs/search/nucstrstr-icc-x86_64-prof.pic.s
delete mode 100644 libs/search/nucstrstr-icc-x86_64-rel.pic.s
delete mode 100644 libs/search/nucstrstr.c
delete mode 100644 libs/search/search-priv.h
delete mode 100644 libs/search/search.c
delete mode 100644 libs/sra/Makefile
delete mode 100644 libs/sra/built-in.vschema
delete mode 100644 libs/sra/libsradb.vers.h
delete mode 100644 libs/sra/reader-abi.c
delete mode 100644 libs/sra/reader-cmn.c
delete mode 100644 libs/sra/reader-cmn.h
delete mode 100644 libs/sra/reader-fastq.c
delete mode 100644 libs/sra/reader-illumina.c
delete mode 100644 libs/sra/reader-sff.c
delete mode 100644 libs/sra/sra-debug.h
delete mode 100644 libs/sra/sra-dflt-schema.c
delete mode 100644 libs/sra/sra-priv.h
delete mode 100644 libs/sra/sra-schema.c
delete mode 100644 libs/sra/sracache.c
delete mode 100644 libs/sra/sracol.c
delete mode 100644 libs/sra/sramgr-cmn.c
delete mode 100644 libs/sra/sramgr.c
delete mode 100644 libs/sra/sraschema-priv.h
delete mode 100644 libs/sra/sraschema-stub.c
delete mode 100644 libs/sra/sraschema.c
delete mode 100644 libs/sra/sratbl-cmn.c
delete mode 100644 libs/sra/sratbl.c
delete mode 100644 libs/sra/types.c
delete mode 100644 libs/sra/wsramgr.c
delete mode 100644 libs/sra/wsraschema-stub.c
delete mode 100644 libs/sra/wsratbl.c
delete mode 100644 libs/sraxf/Makefile
delete mode 100644 libs/sraxf/bio-start.c
delete mode 100644 libs/sraxf/color-from-dna.c
delete mode 100644 libs/sraxf/denormalize.c
delete mode 100644 libs/sraxf/dna-from-color.c
delete mode 100644 libs/sraxf/dynamic-454-read-descriptor.c
delete mode 100644 libs/sraxf/extract-coordinates.c
delete mode 100644 libs/sraxf/extract-name_coord.c
delete mode 100644 libs/sraxf/extract-name_fmt.c
delete mode 100644 libs/sraxf/extract-spot_name.c
delete mode 100644 libs/sraxf/fix_read_seg_impl.h
delete mode 100644 libs/sraxf/format-spot-name.c
delete mode 100644 libs/sraxf/fpcodec.c
delete mode 100644 libs/sraxf/index_lookup.c
delete mode 100644 libs/sraxf/make-position.c
delete mode 100644 libs/sraxf/name-tokenizer.h
delete mode 100644 libs/sraxf/normalize.c
delete mode 100644 libs/sraxf/prefix-tree-to-name.c
delete mode 100644 libs/sraxf/process-position.c
delete mode 100644 libs/sraxf/qual4_codec.h
delete mode 100644 libs/sraxf/qual4_decode.c
delete mode 100644 libs/sraxf/qual4_encode.c
delete mode 100644 libs/sraxf/read-desc.c
delete mode 100644 libs/sraxf/read-seg-from-readn.c
delete mode 100644 libs/sraxf/rewrite-spot-name.c
delete mode 100644 libs/sraxf/rotate.c
delete mode 100644 libs/sraxf/spot-desc.c
delete mode 100644 libs/sraxf/stats.c
delete mode 100644 libs/sraxf/stats_quality.c
delete mode 100644 libs/sraxf/swap.c
delete mode 100644 libs/sraxf/tokenize-spot_name-454.c
delete mode 100644 libs/sraxf/tokenize-spot_name-abi.c
delete mode 100644 libs/sraxf/tokenize-spot_name-helicos.c
delete mode 100644 libs/sraxf/tokenize-spot_name-illumina.c
delete mode 100644 libs/sraxf/tokenize-spot_name-ion-torrent.c
delete mode 100644 libs/sraxf/untyped-priv.h
delete mode 100644 libs/sraxf/untyped.c
delete mode 100644 libs/sraxf/v0-decompress-init.c
delete mode 100644 libs/sraxf/v0-decompress-local.h
delete mode 100644 libs/sraxf/v0-decompress.c
delete mode 100644 libs/sraxf/v0-decompress.h
delete mode 100644 libs/sraxf/v0-funcs.c
delete mode 100644 libs/sraxf/varloc.c
delete mode 100644 libs/vdb/Makefile
delete mode 100644 libs/vdb/blob-headers.c
delete mode 100644 libs/vdb/blob-headers.h
delete mode 100644 libs/vdb/blob-priv.h
delete mode 100644 libs/vdb/blob.c
delete mode 100644 libs/vdb/blob.h
delete mode 100644 libs/vdb/cast.c
delete mode 100644 libs/vdb/column-cmn.c
delete mode 100644 libs/vdb/column-priv.h
delete mode 100644 libs/vdb/column.c
delete mode 100644 libs/vdb/compare.c
delete mode 100644 libs/vdb/cursor-cmn.c
delete mode 100644 libs/vdb/cursor-priv.h
delete mode 100644 libs/vdb/cursor.c
delete mode 100644 libs/vdb/database-cmn.c
delete mode 100644 libs/vdb/database-depend.c
delete mode 100644 libs/vdb/database-load.c
delete mode 100644 libs/vdb/database-priv.h
delete mode 100644 libs/vdb/database.c
delete mode 100644 libs/vdb/dbmgr-cmn.c
delete mode 100644 libs/vdb/dbmgr-priv.h
delete mode 100644 libs/vdb/dbmgr.c
delete mode 100644 libs/vdb/delta_average.c
delete mode 100644 libs/vdb/environment-read.c
delete mode 100644 libs/vdb/fixed-row-len.c
delete mode 100644 libs/vdb/index_insert.c
delete mode 100644 libs/vdb/index_lookup.c
delete mode 100644 libs/vdb/index_project.c
delete mode 100644 libs/vdb/libvdb.vers.h
delete mode 100644 libs/vdb/libwvdb.vers.h
delete mode 100644 libs/vdb/linker-cmn.c
delete mode 100644 libs/vdb/linker-int.c
delete mode 100644 libs/vdb/linker-priv.h
delete mode 100644 libs/vdb/linker.c
delete mode 100644 libs/vdb/merge.c
delete mode 100644 libs/vdb/meta-append.c
delete mode 100644 libs/vdb/meta-attr-read.c
delete mode 100644 libs/vdb/meta-attr-write.c
delete mode 100644 libs/vdb/meta-read.c
delete mode 100644 libs/vdb/meta-value.c
delete mode 100644 libs/vdb/meta-write.c
delete mode 100644 libs/vdb/page-map.c
delete mode 100644 libs/vdb/page-map.h
delete mode 100644 libs/vdb/parameter-read.c
delete mode 100644 libs/vdb/phys-cmn.c
delete mode 100644 libs/vdb/phys-load.c
delete mode 100644 libs/vdb/phys-priv.h
delete mode 100644 libs/vdb/phys.c
delete mode 100644 libs/vdb/prod-cmn.c
delete mode 100644 libs/vdb/prod-expr.c
delete mode 100644 libs/vdb/prod-expr.h
delete mode 100644 libs/vdb/prod-func.c
delete mode 100644 libs/vdb/prod-priv.h
delete mode 100644 libs/vdb/prod.c
delete mode 100644 libs/vdb/range-validate.c
delete mode 100644 libs/vdb/redimension.c
delete mode 100644 libs/vdb/report-vdb.c
delete mode 100644 libs/vdb/row-id.c
delete mode 100644 libs/vdb/row-len.c
delete mode 100644 libs/vdb/schema-db.c
delete mode 100644 libs/vdb/schema-dump.c
delete mode 100644 libs/vdb/schema-dump.h
delete mode 100644 libs/vdb/schema-eval.c
delete mode 100644 libs/vdb/schema-expr.c
delete mode 100644 libs/vdb/schema-expr.h
delete mode 100644 libs/vdb/schema-func.c
delete mode 100644 libs/vdb/schema-int.c
delete mode 100644 libs/vdb/schema-parse.c
delete mode 100644 libs/vdb/schema-parse.h
delete mode 100644 libs/vdb/schema-priv.h
delete mode 100644 libs/vdb/schema-prod.c
delete mode 100644 libs/vdb/schema-tbl.c
delete mode 100644 libs/vdb/schema-tok.c
delete mode 100644 libs/vdb/schema-tok.h
delete mode 100644 libs/vdb/schema-type.c
delete mode 100644 libs/vdb/schema.c
delete mode 100644 libs/vdb/split.c
delete mode 100644 libs/vdb/table-cmn.c
delete mode 100644 libs/vdb/table-load.c
delete mode 100644 libs/vdb/table-priv.h
delete mode 100644 libs/vdb/table.c
delete mode 100644 libs/vdb/transpose.c
delete mode 100644 libs/vdb/wcolumn.c
delete mode 100644 libs/vdb/wcursor.c
delete mode 100644 libs/vdb/wdatabase.c
delete mode 100644 libs/vdb/wdbmgr.c
delete mode 100644 libs/vdb/wlinker.c
delete mode 100644 libs/vdb/wphys.c
delete mode 100644 libs/vdb/wprod.c
delete mode 100644 libs/vdb/wtable.c
delete mode 100644 libs/vdb/xform-priv.h
delete mode 100644 libs/vfs/Makefile
delete mode 100644 libs/vfs/keyring.c
delete mode 100644 libs/vfs/keyring.h
delete mode 100644 libs/vfs/manager.c
delete mode 100644 libs/vfs/path-priv.h
delete mode 100644 libs/vfs/path.c
delete mode 100644 libs/vfs/resolver-priv.h
delete mode 100644 libs/vfs/resolver.c
delete mode 100644 libs/vfs/srapath-stub.c
delete mode 100644 libs/vfs/srapath.c
delete mode 100644 libs/vfs/unix/syskeyring.c
delete mode 100644 libs/vfs/unix/syspath.c
delete mode 100644 libs/vfs/win/syskeyring.c
delete mode 100644 libs/vfs/win/syspath.c
delete mode 100644 libs/vxf/Makefile
delete mode 100644 libs/vxf/add-row-id.c
delete mode 100644 libs/vxf/bit_or.c
delete mode 100644 libs/vxf/bunzip.c
delete mode 100644 libs/vxf/bzip.c
delete mode 100644 libs/vxf/ceil.c
delete mode 100644 libs/vxf/checksum.c
delete mode 100644 libs/vxf/clip.c
delete mode 100644 libs/vxf/cut.c
delete mode 100644 libs/vxf/delta.c
delete mode 100644 libs/vxf/deriv.c
delete mode 100644 libs/vxf/diff.c
delete mode 100644 libs/vxf/echo.c
delete mode 100644 libs/vxf/exists.c
delete mode 100644 libs/vxf/extract_token.c
delete mode 100644 libs/vxf/floor.c
delete mode 100644 libs/vxf/fsplit-join.impl.h
delete mode 100644 libs/vxf/funzip.c
delete mode 100644 libs/vxf/fzip.c
delete mode 100644 libs/vxf/integral.c
delete mode 100644 libs/vxf/integral_0.c
delete mode 100644 libs/vxf/irzip.c
delete mode 100644 libs/vxf/irzip.impl.h
delete mode 100644 libs/vxf/iunzip.c
delete mode 100644 libs/vxf/izip-common.h
delete mode 100644 libs/vxf/izip-decode.impl.h
delete mode 100644 libs/vxf/izip-encode.impl.h
delete mode 100644 libs/vxf/izip.c
delete mode 100644 libs/vxf/lower-case-tech-reads.c
delete mode 100644 libs/vxf/map.c
delete mode 100644 libs/vxf/math-funcs-impl.h
delete mode 100644 libs/vxf/max.c
delete mode 100644 libs/vxf/min.c
delete mode 100644 libs/vxf/outlier-decoder.c
delete mode 100644 libs/vxf/outlier-encoder.c
delete mode 100644 libs/vxf/pack.c
delete mode 100644 libs/vxf/paste.c
delete mode 100644 libs/vxf/rand_4na_2na.c
delete mode 100644 libs/vxf/rldecode.c
delete mode 100644 libs/vxf/rlencode.c
delete mode 100644 libs/vxf/round.c
delete mode 100644 libs/vxf/simple-sub-select.c
delete mode 100644 libs/vxf/sprintf.c
delete mode 100644 libs/vxf/strtonum.c
delete mode 100644 libs/vxf/subtract-row-id.c
delete mode 100644 libs/vxf/sum.c
delete mode 100644 libs/vxf/trim.c
delete mode 100644 libs/vxf/trunc.c
delete mode 100644 libs/vxf/undelta.c
delete mode 100644 libs/vxf/unpack.c
delete mode 100644 libs/vxf/unzip.c
delete mode 100644 libs/vxf/vec-sum.c
delete mode 100644 libs/vxf/wgs-tokenize-accession.c
delete mode 100644 libs/vxf/zip.c
delete mode 100644 libs/wgsxf/Makefile
delete mode 100644 libs/wgsxf/build_read_type.c
delete mode 100644 libs/wgsxf/build_scaffold.c
create mode 100644 os-arch.perl
create mode 100644 os-arch.pm
create mode 100644 package.pm
create mode 100644 test/Makefile
create mode 100644 tools/.gitignore
create mode 100644 tools/align-info/align-info.vers.h
create mode 100644 tools/bam-loader/bam-loader3.c
create mode 100644 tools/bam-loader/bam-reader.c
create mode 100644 tools/bam-loader/bam-reader.h
create mode 100644 tools/bam-loader/loader-imp3.c
create mode 100644 tools/bam-loader/loader-imp3.h
create mode 100644 tools/cache-mgr/cache-mgr.vers.h
create mode 100644 tools/ccextract/Makefile
create mode 100644 tools/ccextract/ccextract.c
create mode 100644 tools/ccextract/ccextract.vers
create mode 100644 tools/cg-dump/Makefile
create mode 100644 tools/cg-dump/cg-dump.c
create mode 100644 tools/cg-dump/cg-dump.vers
create mode 100644 tools/cg-dump/last_rowid.c
create mode 100644 tools/cg-dump/last_rowid.h
create mode 100644 tools/cg-dump/line_token_iter.c
create mode 100644 tools/cg-dump/line_token_iter.h
create mode 100644 tools/cg-dump/num-gen.c
copy tools/{vdb-copy => cg-dump}/num-gen.h (100%)
create mode 100644 tools/cg-dump/progressbar.c
copy tools/{vdb-copy => cg-dump}/progressbar.h (100%)
create mode 100644 tools/cg-dump/sg_lookup.c
create mode 100644 tools/cg-dump/sg_lookup.h
create mode 100644 tools/cg-load/.gitignore
create mode 100644 tools/cg-load/factory-tag-lfr.c
create mode 100644 tools/cg-load/factory-tag-lfr.h
create mode 100644 tools/check-blob-size/Makefile
create mode 100644 tools/check-blob-size/check-blob-size.c
create mode 100644 tools/check-blob-size/check-blob-size.vers
create mode 100644 tools/copycat/Makefile
create mode 100644 tools/copycat/ccbuffer.c
create mode 100644 tools/copycat/ccbuffermgr.c
create mode 100644 tools/copycat/ccbufferq.c
create mode 100644 tools/copycat/cccat.c
create mode 100644 tools/copycat/cccopier.c
create mode 100644 tools/copycat/cccopy.c
create mode 100644 tools/copycat/ccfile.c
create mode 100644 tools/copycat/ccfileformat.c
create mode 100644 tools/copycat/ccproc.c
create mode 100644 tools/copycat/ccprocone.c
create mode 100644 tools/copycat/ccread.c
create mode 100644 tools/copycat/ccsra.c
create mode 100644 tools/copycat/ccsubchunk.c
create mode 100644 tools/copycat/cctar.c
create mode 100644 tools/copycat/cctree-dump.c
create mode 100644 tools/copycat/cctree-priv.h
create mode 100644 tools/copycat/cctree.c
create mode 100644 tools/copycat/copycat-priv.h
create mode 100644 tools/copycat/copycat.c
create mode 100644 tools/copycat/copycat.vers
create mode 100644 tools/copycat/debug.h
create mode 100644 tools/deseq/Makefile
create mode 100644 tools/deseq/csra-trim.vers
create mode 100644 tools/deseq/deseq.c
create mode 100644 tools/fastq-dump/Makefile
create mode 100644 tools/fastq-dump/args.cpp
create mode 100644 tools/fastq-dump/args.hpp
create mode 100644 tools/fastq-dump/fastq-dump.cpp
create mode 100644 tools/fastq-dump/fastq-dump.vers
create mode 100644 tools/fastq-dump/filters.cpp
create mode 100644 tools/fastq-dump/filters.hpp
create mode 100644 tools/fastq-dump/koutstream
create mode 100644 tools/fastq-loader/.gitignore
create mode 100644 tools/fastq-loader/latf-load.vers.h
create mode 100644 tools/fix-run-stat/Makefile
create mode 100644 tools/fix-run-stat/fix-run-stat.c
create mode 100644 tools/fix-run-stat/fix-run-stat.vers
create mode 100644 tools/fuse/Makefile
create mode 100644 tools/fuse/accessor.c
create mode 100644 tools/fuse/accessor.h
create mode 100644 tools/fuse/debug.h
create mode 100644 tools/fuse/directory.c
create mode 100644 tools/fuse/directory.h
create mode 100644 tools/fuse/dump-idx.c
create mode 100644 tools/fuse/dump-idx.vers
create mode 100644 tools/fuse/dump-idx.vers.h
create mode 100644 tools/fuse/file.c
create mode 100644 tools/fuse/file.h
create mode 100644 tools/fuse/formats.c
create mode 100644 tools/fuse/formats.h
create mode 100644 tools/fuse/kfile-accessor.c
create mode 100644 tools/fuse/kfile-accessor.h
create mode 100644 tools/fuse/log.c
create mode 100644 tools/fuse/log.h
create mode 100644 tools/fuse/node.c
create mode 100644 tools/fuse/node.h
create mode 100644 tools/fuse/remote-cache.c
create mode 100644 tools/fuse/remote-cache.h
create mode 100644 tools/fuse/remote-directory.c
create mode 100644 tools/fuse/remote-directory.h
create mode 100644 tools/fuse/remote-file.c
create mode 100644 tools/fuse/remote-file.h
create mode 100644 tools/fuse/remote-fuser.c
create mode 100644 tools/fuse/remote-fuser.h
create mode 100644 tools/fuse/remote-fuser.vers
create mode 100644 tools/fuse/remote-link.c
create mode 100644 tools/fuse/remote-link.h
create mode 100644 tools/fuse/remote-xml.c
create mode 100644 tools/fuse/remote-xml.h
create mode 100644 tools/fuse/sra-directory.c
create mode 100644 tools/fuse/sra-directory.h
create mode 100644 tools/fuse/sra-fastq.c
create mode 100644 tools/fuse/sra-fastq.h
create mode 100644 tools/fuse/sra-fuser-test.c
create mode 100644 tools/fuse/sra-fuser-test.vers
create mode 100644 tools/fuse/sra-fuser-test.vers.h
create mode 100644 tools/fuse/sra-fuser.c
create mode 100644 tools/fuse/sra-fuser.h
create mode 100644 tools/fuse/sra-fuser.vers
create mode 100644 tools/fuse/sra-fuser.xsd
create mode 100644 tools/fuse/sra-list.c
create mode 100644 tools/fuse/sra-list.h
create mode 100644 tools/fuse/sra-makeidx.c
create mode 100644 tools/fuse/sra-makeidx.vers
create mode 100644 tools/fuse/sra-node.c
create mode 100644 tools/fuse/sra-node.h
create mode 100644 tools/fuse/sra-sff.c
create mode 100644 tools/fuse/sra-sff.h
create mode 100644 tools/fuse/tar-file.c
create mode 100644 tools/fuse/tar-file.h
create mode 100644 tools/fuse/tar-list.c
create mode 100644 tools/fuse/tar-list.h
create mode 100644 tools/fuse/tar-node.c
create mode 100644 tools/fuse/tar-node.h
create mode 100644 tools/fuse/text-file.c
create mode 100644 tools/fuse/text-file.h
create mode 100644 tools/fuse/unix/remote-fuser-sys.c
create mode 100644 tools/fuse/unix/sra-fuser-sys.c
create mode 100644 tools/fuse/xml.c
create mode 100644 tools/fuse/xml.h
create mode 100644 tools/fuse/zlib-simple.c
create mode 100644 tools/fuse/zlib-simple.h
create mode 100644 tools/kar/kar.vers.h
create mode 100644 tools/kar/sra-kar.vers.h
create mode 100644 tools/keyring-srv/Makefile
create mode 100644 tools/keyring-srv/keyring-data.c
create mode 100644 tools/keyring-srv/keyring-data.h
create mode 100644 tools/keyring-srv/keyring-database.c
create mode 100644 tools/keyring-srv/keyring-database.h
create mode 100644 tools/keyring-srv/keyring-srv-main.c
create mode 100644 tools/keyring-srv/keyring-srv.c
create mode 100644 tools/keyring-srv/keyring-srv.h
create mode 100644 tools/keyring-srv/keyring-srv.vers
create mode 100644 tools/kqsh/.gitignore
create mode 100644 tools/kqsh/Makefile
create mode 100644 tools/kqsh/kqsh-alter.c
create mode 100644 tools/kqsh/kqsh-close.c
create mode 100644 tools/kqsh/kqsh-create.c
create mode 100644 tools/kqsh/kqsh-help.c
create mode 100644 tools/kqsh/kqsh-load.c
create mode 100644 tools/kqsh/kqsh-open.c
create mode 100644 tools/kqsh/kqsh-parse.c
create mode 100644 tools/kqsh/kqsh-print.c
create mode 100644 tools/kqsh/kqsh-priv.h
create mode 100644 tools/kqsh/kqsh-show.c
create mode 100755 tools/kqsh/kqsh-thunk.pl
create mode 100644 tools/kqsh/kqsh-tok.c
create mode 100644 tools/kqsh/kqsh-tok.h
create mode 100644 tools/kqsh/kqsh-write.c
create mode 100644 tools/kqsh/kqsh.c
create mode 100644 tools/kqsh/kqsh.vers
create mode 100644 tools/meta-sync/Makefile
create mode 100644 tools/meta-sync/meta-sync.c
create mode 100755 tools/meta-sync/meta-sync.pl
create mode 100644 tools/meta-sync/meta-sync.vers
create mode 100644 tools/pacbio-load/.gitignore
create mode 100644 tools/pacbio-load/Makefile
create mode 100644 tools/pacbio-load/pacbio-load.c
create mode 100644 tools/pacbio-load/pacbio-load.vers
create mode 100644 tools/pacbio-load/pl-basecalls_cmn.c
create mode 100644 tools/pacbio-load/pl-basecalls_cmn.h
create mode 100644 tools/pacbio-load/pl-consensus.c
create mode 100644 tools/pacbio-load/pl-consensus.h
create mode 100644 tools/pacbio-load/pl-context.c
create mode 100644 tools/pacbio-load/pl-context.h
create mode 100644 tools/pacbio-load/pl-metrics.c
create mode 100644 tools/pacbio-load/pl-metrics.h
create mode 100644 tools/pacbio-load/pl-passes.c
create mode 100644 tools/pacbio-load/pl-passes.h
create mode 100644 tools/pacbio-load/pl-progress.c
create mode 100644 tools/pacbio-load/pl-progress.h
create mode 100644 tools/pacbio-load/pl-regions.c
create mode 100644 tools/pacbio-load/pl-regions.h
create mode 100644 tools/pacbio-load/pl-sequence.c
create mode 100644 tools/pacbio-load/pl-sequence.h
create mode 100644 tools/pacbio-load/pl-tools.c
create mode 100644 tools/pacbio-load/pl-tools.h
create mode 100644 tools/pacbio-load/pl-zmw.c
create mode 100644 tools/pacbio-load/pl-zmw.h
create mode 100755 tools/pacbio-load/verify/ins_nl.pl
create mode 100755 tools/pacbio-load/verify/ins_nl_1.pl
create mode 100755 tools/pacbio-load/verify/ins_nl_2.pl
create mode 100755 tools/pacbio-load/verify/ins_nl_4.pl
create mode 100755 tools/pacbio-load/verify/ins_nl_f.pl
create mode 100644 tools/prefetch/prefetch.vers.h
create mode 100644 tools/qual-recal/Makefile
create mode 100644 tools/qual-recal/make_histo_data.sh
create mode 100644 tools/qual-recal/qual-recal.c
create mode 100644 tools/qual-recalib-stat/.gitignore
create mode 100644 tools/qual-recalib-stat/Makefile
create mode 100644 tools/qual-recalib-stat/columns.c
create mode 100644 tools/qual-recalib-stat/columns.h
create mode 100644 tools/qual-recalib-stat/context.c
create mode 100644 tools/qual-recalib-stat/context.h
create mode 100755 tools/qual-recalib-stat/fasta_dump.pl
copy tools/{vdb-copy => qual-recalib-stat}/namelist_tools.c (100%)
create mode 100644 tools/qual-recalib-stat/namelist_tools.h
create mode 100644 tools/qual-recalib-stat/num-gen.c
copy tools/{vdb-copy => qual-recalib-stat}/num-gen.h (100%)
create mode 100644 tools/qual-recalib-stat/progressbar.c
create mode 100644 tools/qual-recalib-stat/progressbar.h
create mode 100644 tools/qual-recalib-stat/qual-recalib-stat.c
create mode 100644 tools/qual-recalib-stat/qual-recalib-stat.vers
create mode 100644 tools/qual-recalib-stat/qual-recalib-stat.vers.h
create mode 100644 tools/qual-recalib-stat/reader.c
create mode 100644 tools/qual-recalib-stat/reader.h
create mode 100644 tools/qual-recalib-stat/ref_exclude.c
create mode 100644 tools/qual-recalib-stat/ref_exclude.h
create mode 100755 tools/qual-recalib-stat/ref_grab.pl
create mode 100644 tools/qual-recalib-stat/spot_position.c
create mode 100644 tools/qual-recalib-stat/spot_position.h
create mode 100644 tools/qual-recalib-stat/stat_mod.c
create mode 100644 tools/qual-recalib-stat/stat_mod.h
create mode 100644 tools/qual-recalib-stat/stat_mod_1.c
create mode 100644 tools/qual-recalib-stat/stat_mod_1.h
create mode 100644 tools/qual-recalib-stat/stat_mod_2.c
create mode 100644 tools/qual-recalib-stat/stat_mod_2.h
create mode 100644 tools/qual-recalib-stat/writer.c
create mode 100644 tools/qual-recalib-stat/writer.h
create mode 100644 tools/rd-filter-redact/Makefile
create mode 100644 tools/rd-filter-redact/rd-filter-redact.c
create mode 100644 tools/rd-filter-redact/rd-filter-redact.vers
create mode 100644 tools/rd-filter-redact/read-filter-redact.c
create mode 100644 tools/rd-filter-redact/read-filter-redact.vers
create mode 100644 tools/rd-filter-redact/read-filter-redact.vers.h
create mode 100644 tools/rd-filter-redact/test-read-write-cursor.c
create mode 100644 tools/rd-filter-redact/test-read-write-cursor.vers
create mode 100644 tools/run-stat/.gitignore
create mode 100644 tools/run-stat/Makefile
create mode 100644 tools/run-stat/chart.c
create mode 100644 tools/run-stat/chart.h
create mode 100644 tools/run-stat/context.c
create mode 100644 tools/run-stat/context.h
create mode 100644 tools/run-stat/definitions.h
create mode 100644 tools/run-stat/helper.c
create mode 100644 tools/run-stat/helper.h
create mode 100644 tools/run-stat/key_value.c
create mode 100644 tools/run-stat/key_value.h
create mode 100644 tools/run-stat/mod_cmn.c
create mode 100644 tools/run-stat/mod_cmn.h
create mode 100644 tools/run-stat/mod_reads.c
create mode 100644 tools/run-stat/mod_reads.h
create mode 100644 tools/run-stat/mod_reads_defs.h
create mode 100644 tools/run-stat/mod_reads_helper.c
create mode 100644 tools/run-stat/mod_reads_helper.h
create mode 100644 tools/run-stat/num-gen.c
create mode 100644 tools/run-stat/num-gen.h
create mode 100644 tools/run-stat/progressbar.c
create mode 100644 tools/run-stat/progressbar.h
create mode 100644 tools/run-stat/rd_filter.c
create mode 100644 tools/run-stat/rd_filter.h
create mode 100644 tools/run-stat/run-stat.c
create mode 100644 tools/run-stat/run-stat.vers
create mode 100644 tools/run-stat/svg.c
create mode 100644 tools/run-stat/svg.h
create mode 100644 tools/sra-dump/.gitignore
create mode 100644 tools/sra-dump/abi-dump.vers.h
create mode 100644 tools/sra-dump/fastq-dump.vers.h
create mode 100644 tools/sra-dump/illumina-dump.vers.h
create mode 100644 tools/sra-dump/sff-dump.vers.h
create mode 100644 tools/sra-load/pacbio-fmt.c
create mode 100644 tools/sra-pileup/.gitignore
create mode 100644 tools/sra-pileup/4na_ascii.c
create mode 100644 tools/sra-pileup/4na_ascii.h
create mode 100644 tools/sra-pileup/dyn_string.c
create mode 100644 tools/sra-pileup/dyn_string.h
create mode 100755 tools/sra-pileup/make_opt.pl
create mode 100644 tools/sra-pileup/perf_log.c
create mode 100644 tools/sra-pileup/perf_log.h
create mode 100644 tools/sra-pileup/pileup_counters.c
create mode 100644 tools/sra-pileup/pileup_counters.h
create mode 100644 tools/sra-pileup/pileup_index.c
create mode 100644 tools/sra-pileup/pileup_index.h
create mode 100644 tools/sra-pileup/pileup_options.h
create mode 100644 tools/sra-pileup/pileup_stat.c
create mode 100644 tools/sra-pileup/pileup_stat.h
create mode 100644 tools/sra-pileup/pileup_v2.c
create mode 100644 tools/sra-pileup/pileup_v2.h
create mode 100644 tools/sra-pileup/pileup_varcount.c
create mode 100644 tools/sra-pileup/pileup_varcount.h
create mode 100644 tools/sra-pileup/ref_walker_0.c
create mode 100644 tools/sra-pileup/ref_walker_0.h
create mode 100644 tools/sra-pileup/report_deletes.c
create mode 100644 tools/sra-pileup/report_deletes.h
create mode 100644 tools/sra-pileup/rna_splice_log.c
create mode 100644 tools/sra-pileup/rna_splice_log.h
create mode 100644 tools/sra-pileup/sam-dump.vers.h
create mode 100644 tools/sra-pileup/sam-dump2.vers
copy tools/{bam-loader/bam-load.3.vers => sra-pileup/sam-dump3.vers} (100%)
create mode 100755 tools/sra-pileup/splitfastq.pl
create mode 100644 tools/sra-pileup/sra-pileup.vers.h
create mode 100644 tools/sra-pileup/walk_debug.c
create mode 100644 tools/sra-pileup/walk_debug.h
create mode 100644 tools/sra-pileup/writer.c
create mode 100644 tools/sra-pileup/writer.h
create mode 100644 tools/sra-shell/Makefile
create mode 100644 tools/sra-shell/guilib/Makefile
create mode 100644 tools/sra-shell/job-exec/Makefile
create mode 100644 tools/sra-shell/parser/Makefile
create mode 100644 tools/sra-shell/parser/sra-shell-lex.l
create mode 100644 tools/sra-shell/parser/sra-shell.y
create mode 100644 tools/sra-shell/sra-gui/Makefile
create mode 100644 tools/sra-shell/sra-gui/sra-gui.c
create mode 100644 tools/sra-shell/sra-gui/sra-gui.vers
create mode 100644 tools/sra-shell/sra-shell/Makefile
create mode 100644 tools/sra-shell/sra-shell/sra-shell.c
create mode 100644 tools/sra-shell/sra-shell/sra-shell.vers
create mode 100644 tools/sra-shell/turboVision/Makefile
create mode 100644 tools/sra-stat/sra-stat.vers.h
create mode 100644 tools/sra/Makefile
create mode 100644 tools/sra/sra-dbcc.c
create mode 100644 tools/sra/table-vers.c
create mode 100644 tools/sra/table-vers.vers
create mode 100644 tools/srapath/srapath.vers.h
create mode 100644 tools/update-schema/Makefile
create mode 100644 tools/update-schema/update-schema.c
create mode 100644 tools/update-schema/vdb-update-schema.vers
create mode 100644 tools/util/crc32sum.c
create mode 100644 tools/util/kdbmeta.vers.h
create mode 100644 tools/util/md5cp.c
create mode 100644 tools/util/md5cp.vers.h
create mode 100644 tools/util/pacbio-correct.c
create mode 100644 tools/util/pacbio-correct.vers
create mode 100644 tools/util/rcexplain.vers.h
create mode 100644 tools/util/schema-replace.c
create mode 100755 tools/util/schema-replace.sh
create mode 100644 tools/util/schema-replace.vers.h
create mode 100644 tools/util/sortreadtest.c
create mode 100644 tools/util/test-sra.vers.h
create mode 100644 tools/util/vdb-lock.vers.h
create mode 100644 tools/util/vdb-passwd.vers.h
create mode 100644 tools/util/vdb-unlock.vers.h
create mode 100644 tools/vcf-loader/Makefile
create mode 100644 tools/vcf-loader/vcf-database.c
create mode 100644 tools/vcf-loader/vcf-database.h
create mode 100644 tools/vcf-loader/vcf-grammar.c
create mode 100644 tools/vcf-loader/vcf-grammar.h
create mode 100644 tools/vcf-loader/vcf-grammar.y
create mode 100644 tools/vcf-loader/vcf-lex.c
create mode 100644 tools/vcf-loader/vcf-lex.l
create mode 100644 tools/vcf-loader/vcf-load.vers
create mode 100644 tools/vcf-loader/vcf-loader.c
create mode 100644 tools/vcf-loader/vcf-parse.h
create mode 100644 tools/vcf-loader/vcf-reader.c
create mode 100644 tools/vcf-loader/vcf-reader.h
create mode 100644 tools/vdb-config/configure.cpp
create mode 100644 tools/vdb-config/configure.h
create mode 100644 tools/vdb-config/interactive.cpp
create mode 100644 tools/vdb-config/interactive.h
create mode 100644 tools/vdb-config/util.cpp
create mode 100644 tools/vdb-config/util.hpp
create mode 100644 tools/vdb-config/vdb-config-model.cpp
create mode 100644 tools/vdb-config/vdb-config-model.hpp
create mode 100644 tools/vdb-config/vdb-config.vers.h
create mode 100644 tools/vdb-config/vdb-config2.cpp
create mode 100644 tools/vdb-config/vdb-config2.h
create mode 100644 tools/vdb-copy/.gitignore
create mode 100644 tools/vdb-copy/column_match.c
create mode 100644 tools/vdb-copy/column_match.h
create mode 100644 tools/vdb-copy/copy_context.c
create mode 100644 tools/vdb-copy/copy_context.h
create mode 100644 tools/vdb-copy/vdb-copy.vers.h
create mode 100644 tools/vdb-decrypt/vdb-decrypt.vers.h
create mode 100644 tools/vdb-decrypt/vdb-encrypt.vers.h
create mode 100644 tools/vdb-dump/.gitignore
create mode 100644 tools/vdb-dump/help.txt
create mode 100644 tools/vdb-dump/vdb-boot.c
create mode 100644 tools/vdb-dump/vdb-boot.vers
create mode 100644 tools/vdb-dump/vdb-boot.vschema
create mode 100644 tools/vdb-dump/vdb-dump-bin.c
create mode 100644 tools/vdb-dump/vdb-dump-bin.h
create mode 100644 tools/vdb-dump/vdb-dump-print.c
create mode 100644 tools/vdb-dump/vdb-dump-print.h
create mode 100644 tools/vdb-dump/vdb-dump.vers.h
create mode 100644 tools/vdb-dump/vdb_info.c
create mode 100644 tools/vdb-dump/vdb_info.h
create mode 100644 tools/vdb-validate/vdb-validate.vers.h
create mode 100644 tools/vdbview/b_first.png
create mode 100644 tools/vdbview/b_goto.png
create mode 100644 tools/vdbview/b_last.png
create mode 100644 tools/vdbview/b_next.png
create mode 100644 tools/vdbview/b_nextpage.png
create mode 100644 tools/vdbview/b_prev.png
create mode 100644 tools/vdbview/b_prevpage.png
create mode 100644 tools/vdbview/b_search.png
create mode 100644 tools/vdbview/background.pas
create mode 100644 tools/vdbview/buttons.svg
create mode 100644 tools/vdbview/columnsel.lfm
create mode 100644 tools/vdbview/columnsel.pas
create mode 100644 tools/vdbview/dataproxy.pas
create mode 100644 tools/vdbview/gotoform.lfm
create mode 100644 tools/vdbview/gotoform.pas
create mode 100644 tools/vdbview/jobdef.pas
create mode 100644 tools/vdbview/linkedlist.pas
create mode 100644 tools/vdbview/logo_128.png
create mode 100644 tools/vdbview/logo_16.png
create mode 100644 tools/vdbview/logo_256.png
create mode 100644 tools/vdbview/logo_32.png
create mode 100644 tools/vdbview/logo_64.png
create mode 100644 tools/vdbview/mainwindow.lfm
create mode 100644 tools/vdbview/mainwindow.pas
create mode 100644 tools/vdbview/searchform.lfm
create mode 100644 tools/vdbview/searchform.pas
create mode 100644 tools/vdbview/selector_types.pas
create mode 100644 tools/vdbview/support_unit.pas
create mode 100644 tools/vdbview/svdb.pas
create mode 100644 tools/vdbview/svdb_obj.pas
create mode 100644 tools/vdbview/vdbview.ico
create mode 100644 tools/vdbview/vdbview.lpi
create mode 100644 tools/vdbview/vdbview.lpr
create mode 100644 tools/vdbview/vdbview.res
create mode 100644 tools/vdbview/vdbview1.ico
create mode 100644 tools/vdbview/version.lfm
create mode 100644 tools/vdbview/version.pas
create mode 100644 tools/vtblcp/Makefile
create mode 100644 tools/vtblcp/vtblcp-priv.h
create mode 100644 tools/vtblcp/vtblcp.c
create mode 100644 tools/vtblcp/vtblcp.vers
create mode 100644 tools/workspace/.gitignore
create mode 100644 tools/workspace/Makefile
create mode 100644 tools/workspace/path-to-kar-file.cpp
create mode 100644 tools/workspace/prefs-lex.l
create mode 100644 tools/workspace/prefs-yacc.y
create mode 100644 tools/workspace/sra.cpp
create mode 100644 tools/workspace/sra.vers
create mode 100644 tools/workspace/sratoolkit-exception.cpp
create mode 100644 tools/workspace/sratoolkit-exception.hpp
create mode 100644 tools/workspace/token.c
create mode 100644 tools/workspace/token.h
create mode 100644 tools/workspace/workspace.cpp
create mode 100644 win-configure.bat
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git
More information about the debian-med-commit
mailing list