[med-svn] [ncbi-vdb] branch master updated (1ee3605 -> c9a9ef2)
Andreas Tille
tille at debian.org
Wed Jan 11 10:10:46 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository ncbi-vdb.
from 1ee3605 Merge tag 'upstream/2.8.1'
new bcf9fd2 New upstream version
new 879c0ec New upstream version 2.8.1+dfsg
new fdd6a91 Merge tag 'upstream/2.8.1+dfsg'
new c9a9ef2 Refresh patches
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.github/ISSUE_TEMPLATE.md | 21 -
.github/PULL_REQUEST_TEMPLATE.md | 13 -
.gitignore | 49 +-
.travis.yml | 20 -
CHANGES.md | 58 +
LICENSE | 77 +
Makefile | 159 +
README.md | 114 +-
build.gradle | 227 -
build.xml | 62 -
build/.gitignore | 10 +
build/Makefile.cc | 67 +
build/Makefile.clang | 80 +
build/Makefile.env | 373 +
build/Makefile.gcc | 88 +
build/Makefile.icc | 77 +
build/Makefile.install | 151 +
build/Makefile.linux | 84 +
build/Makefile.rules | 111 +
build/Makefile.scm | 94 +
build/Makefile.shell | 176 +
build/Makefile.targets | 117 +
build/Makefile.vers | 26 +
build/abspath.sh | 31 +
build/cc.sh | 129 +
build/cp.sh | 32 +
build/gprof2dot.py | 2763 ++
build/increment-release.sh | 44 +
build/ld.linux.cmn.sh | 158 +
build/ld.linux.dlib.sh | 308 +
build/ld.linux.exe.sh | 322 +
build/ld.linux.exe_cmd.sh | 1 +
build/ld.linux.gcc.sh | 47 +
build/ld.linux.icc.sh | 47 +
build/ld.linux.ln.sh | 98 +
build/ld.linux.slib.sh | 146 +
build/ld.mac.clang.sh | 59 +
build/ld.mac.cmn.sh | 159 +
build/ld.mac.dlib.sh | 366 +
build/ld.mac.exe.sh | 340 +
build/ld.mac.gcc.sh | 58 +
build/ld.mac.ln.sh | 103 +
build/ld.mac.slib.sh | 101 +
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 | 593 +
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 | 149 +
build/ld.unix.slib.sh | 124 +
build/ld.win.cmn.sh | 225 +
build/ld.win.dlib.sh | 327 +
build/ld.win.exe.sh | 321 +
build/ld.win.slib.sh | 135 +
build/ld.win.stub.sh | 60 +
build/ld.win.vc++.sh | 65 +
build/libexists.sh | 180 +
build/mac.arch.sh | 87 +
build/make-defs-xf.pl | 108 +
build/make-defs.pl | 247 +
build/make-vers-inc.sh | 46 +
build/run_remotely.sh | 124 +
build/scm-collect.sh | 42 +
build/scm.sh | 136 +
build/scm.txt | 117 +
build/sra-dflt-schema.sh | 163 +
build/tag-module.sh | 213 +
build/valgrind.suppress | 21 +
build/wait_for_file.sh | 65 +
configure | 45 +
debian/changelog | 6 +
debian/patches/find_hdf5_serial.patch | 2 +-
debian/patches/find_ngs-sdk.patch | 4 +-
debian/patches/spelling.patch | 2 +-
gradle/wrapper/gradle-wrapper.jar | Bin 53556 -> 0 bytes
gradle/wrapper/gradle-wrapper.properties | 6 -
gradlew | 164 -
.../tribble/util/ftp => interfaces}/.gitignore | 0
interfaces/align/align-access.h | 350 +
interfaces/align/align.h | 70 +
interfaces/align/align.vschema | 1610 +
interfaces/align/alignsrc.h | 71 +
interfaces/align/bam.h | 836 +
interfaces/align/dna-reverse-cmpl.h | 43 +
interfaces/align/extern.h | 41 +
interfaces/align/iterator.h | 610 +
interfaces/align/iterator_examples.txt | 148 +
interfaces/align/manager.h | 69 +
interfaces/align/mate-cache.vschema | 99 +
interfaces/align/pileup-stats.vschema | 120 +
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 | 88 +
interfaces/align/refseq.vschema | 100 +
interfaces/align/seq.vschema | 300 +
interfaces/align/writer-alignment.h | 181 +
interfaces/align/writer-cmn.h | 46 +
interfaces/align/writer-reference.h | 180 +
interfaces/align/writer-refseq.h | 89 +
interfaces/align/writer-sequence.h | 157 +
interfaces/cc/cc/compiler.h | 39 +
interfaces/cc/gcc/compiler.h | 39 +
interfaces/cc/gcc/fat86/arch-impl.h | 33 +
interfaces/cc/gcc/fat86/atomic.h | 33 +
interfaces/cc/gcc/fat86/atomic32.h | 37 +
interfaces/cc/gcc/fat86/atomic64.h | 32 +
interfaces/cc/gcc/fat86/bitstr.h | 33 +
interfaces/cc/gcc/fat86/byteswap.h | 33 +
interfaces/cc/gcc/fat86/strtol.h | 33 +
interfaces/cc/gcc/i386/arch-impl.h | 488 +
interfaces/cc/gcc/i386/atomic.h | 169 +
interfaces/cc/gcc/i386/atomic32.h | 366 +
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/ppc32/arch-impl.h | 209 +
interfaces/cc/gcc/ppc32/atomic.h | 157 +
interfaces/cc/gcc/ppc32/atomic32.h | 197 +
interfaces/cc/gcc/ppc32/bitstr.h | 40 +
interfaces/cc/gcc/ppc32/strtol.h | 67 +
interfaces/cc/gcc/v128.h | 1093 +
interfaces/cc/gcc/va_copy.h | 49 +
interfaces/cc/gcc/x86_64/arch-impl.h | 459 +
interfaces/cc/gcc/x86_64/atomic.h | 183 +
interfaces/cc/gcc/x86_64/atomic32.h | 365 +
interfaces/cc/gcc/x86_64/atomic64.h | 365 +
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 | 378 +
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/csra2/csra2.vschema | 42 +
interfaces/csra2/read.vschema | 255 +
interfaces/csra2/reference.vschema | 245 +
interfaces/csra2/stats.vschema | 92 +
interfaces/fastq/extern.h | 41 +
interfaces/fastq/fq-dump.h | 110 +
interfaces/hdf5/extern.h | 41 +
interfaces/hdf5/kdf5.h | 89 +
interfaces/insdc/insdc.h | 277 +
interfaces/insdc/insdc.vschema | 232 +
interfaces/insdc/seq.vschema | 210 +
interfaces/insdc/sra.h | 111 +
interfaces/insdc/sra.vschema | 470 +
interfaces/kapp/args-conv.h | 57 +
interfaces/kapp/args.h | 402 +
interfaces/kapp/extern.h | 47 +
interfaces/kapp/loader-file.h | 122 +
interfaces/kapp/loader-meta.h | 55 +
interfaces/kapp/log-xml.h | 76 +
interfaces/kapp/main.h | 174 +
interfaces/kapp/progressbar.h | 82 +
interfaces/kapp/queue-file.h | 149 +
interfaces/kdb/btree.h | 188 +
interfaces/kdb/column.h | 360 +
interfaces/kdb/consistency-check.h | 142 +
interfaces/kdb/database.h | 278 +
interfaces/kdb/extern.h | 41 +
interfaces/kdb/index.h | 309 +
interfaces/kdb/kdb-priv.h | 165 +
interfaces/kdb/manager.h | 182 +
interfaces/kdb/meta.h | 411 +
interfaces/kdb/meta.hpp | 487 +
interfaces/kdb/namelist.h | 81 +
interfaces/kdb/rowset-impl.h | 141 +
interfaces/kdb/rowset.h | 186 +
interfaces/kdb/table.h | 298 +
interfaces/kfc/callconv.h | 53 +
interfaces/kfc/ctx.h | 198 +
interfaces/kfc/defs.h | 199 +
interfaces/kfc/except.h | 215 +
interfaces/kfc/extern.h | 68 +
interfaces/kfc/rc.h | 361 +
interfaces/kfc/refcount-impl.h | 95 +
interfaces/kfc/refcount.h | 246 +
interfaces/kfc/rsrc-global.h | 72 +
interfaces/kfc/rsrc.h | 89 +
interfaces/kfc/tstate.h | 107 +
interfaces/kfc/vtbl-impl.h | 139 +
interfaces/kfc/xc.h | 192 +
interfaces/kfc/xcdefs.h | 81 +
interfaces/kfc/xcext.h | 64 +
interfaces/kfc/xcgen.h | 68 +
interfaces/kfg/config.h | 425 +
interfaces/kfg/extern.h | 41 +
interfaces/kfg/kart.h | 90 +
interfaces/kfg/keystore-priv.h | 92 +
interfaces/kfg/keystore.h | 159 +
interfaces/kfg/kfg-priv.h | 110 +
interfaces/kfg/ngc.h | 67 +
interfaces/kfg/properties.h | 143 +
interfaces/kfg/repository.h | 423 +
interfaces/kfs/arc.h | 143 +
interfaces/kfs/arrayfile.h | 180 +
interfaces/kfs/buffile.h | 94 +
interfaces/kfs/bzip.h | 77 +
interfaces/kfs/cacheteefile.h | 162 +
interfaces/kfs/countfile.h | 73 +
interfaces/kfs/crc.h | 292 +
interfaces/kfs/defs.h | 121 +
interfaces/kfs/directory.h | 591 +
interfaces/kfs/directory.hpp | 582 +
interfaces/kfs/dyload.h | 223 +
interfaces/kfs/extendable-ramfile.h | 50 +
interfaces/kfs/extern.h | 41 +
interfaces/kfs/ffext.h | 48 +
interfaces/kfs/ffmagic.h | 49 +
interfaces/kfs/file-impl.h | 193 +
interfaces/kfs/file-v1.h | 259 +
interfaces/kfs/file-v2.h | 264 +
interfaces/kfs/file.h | 99 +
interfaces/kfs/file.hpp | 147 +
interfaces/kfs/fileformat.h | 140 +
interfaces/kfs/filetools.h | 86 +
interfaces/kfs/gzip.h | 77 +
interfaces/kfs/impl.h | 319 +
interfaces/kfs/kfs-priv.h | 99 +
interfaces/kfs/lockfile.h | 116 +
interfaces/kfs/manager.h | 31 +
interfaces/kfs/md5.h | 289 +
interfaces/kfs/mmap.h | 134 +
interfaces/kfs/nullfile.h | 62 +
interfaces/kfs/pagefile.h | 191 +
interfaces/kfs/path-priv.h | 32 +
interfaces/kfs/path.h | 32 +
interfaces/kfs/pmem.h | 156 +
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/szip.h | 77 +
interfaces/kfs/tar.h | 94 +
interfaces/kfs/teefile.h | 66 +
interfaces/kfs/toc.h | 148 +
interfaces/kfs/wgaencrypt.h | 27 +
interfaces/klib/btree.h | 147 +
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 | 549 +
interfaces/klib/defs.h | 147 +
interfaces/klib/extern.h | 51 +
interfaces/klib/impl.h | 96 +
interfaces/klib/klib-priv.h | 108 +
interfaces/klib/ksort-macro.h | 257 +
interfaces/klib/log.h | 381 +
interfaces/klib/logfmt.h | 62 +
interfaces/klib/misc.h | 51 +
interfaces/klib/namelist.h | 227 +
interfaces/klib/namelist.hpp | 130 +
interfaces/klib/ncbi-vdb-version.h | 56 +
interfaces/klib/num-gen.h | 228 +
interfaces/klib/out.h | 86 +
interfaces/klib/pack.h | 138 +
interfaces/klib/path-priv.h | 266 +
interfaces/klib/path.h | 252 +
interfaces/klib/pbstree.h | 287 +
interfaces/klib/printf.h | 406 +
interfaces/klib/progressbar.h | 85 +
interfaces/klib/ptrie.h | 296 +
interfaces/klib/rc.h | 201 +
interfaces/klib/refcount.h | 102 +
interfaces/klib/report.h | 103 +
interfaces/klib/sort.h | 123 +
interfaces/klib/sra-release-version.h | 100 +
interfaces/klib/status.h | 147 +
interfaces/klib/symbol.h | 146 +
interfaces/klib/symtab.h | 225 +
interfaces/klib/text.h | 563 +
interfaces/klib/time.h | 100 +
interfaces/klib/token.h | 254 +
interfaces/klib/trie.h | 293 +
interfaces/klib/vector.h | 539 +
interfaces/klib/vlen-encode.h | 161 +
interfaces/klib/writer.h | 170 +
interfaces/kns/adapt.h | 89 +
interfaces/kns/ascp.h | 101 +
interfaces/kns/endpoint.h | 148 +
interfaces/kns/extern.h | 41 +
interfaces/kns/http-priv.h | 63 +
interfaces/kns/http.h | 407 +
interfaces/kns/impl.h | 111 +
interfaces/kns/kns-mgr-priv.h | 149 +
interfaces/kns/manager-ext.h | 59 +
interfaces/kns/manager.h | 103 +
interfaces/kns/socket.h | 151 +
interfaces/kns/stream.h | 222 +
interfaces/kns/tls.h | 100 +
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 | 120 +
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 | 74 +
interfaces/krypto/aes-priv.h | 1 +
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 | 94 +
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 | 260 +
interfaces/ktst/unit_test_suite.hpp | 515 +
interfaces/kxml/xml.h | 382 +
interfaces/kxml/xml.hpp | 198 +
interfaces/loader/alignment-writer.h | 108 +
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 | 80 +
interfaces/loader/sequence-writer.h | 93 +
interfaces/ncbi/clip.vschema | 147 +
interfaces/ncbi/extern.h | 41 +
interfaces/ncbi/kimpl-sra-cgi.h | 91 +
interfaces/ncbi/ksra-cgi-lib.h | 52 +
interfaces/ncbi/ksra-cgi.h | 111 +
interfaces/ncbi/ncbi.h | 73 +
interfaces/ncbi/ncbi.vschema | 195 +
interfaces/ncbi/pnbrdb.vschema | 98 +
interfaces/ncbi/seq-graph.vschema | 180 +
interfaces/ncbi/seq.vschema | 894 +
interfaces/ncbi/spotname.h | 150 +
interfaces/ncbi/spotname.vschema | 377 +
interfaces/ncbi/sra.vschema | 758 +
interfaces/ncbi/stats.vschema | 119 +
interfaces/ncbi/varloc.vschema | 204 +
interfaces/ncbi/vdb-blast-priv.h | 53 +
interfaces/ncbi/vdb-blast.h | 606 +
interfaces/ncbi/wgs-contig.h | 183 +
interfaces/ncbi/wgs-contig.vschema | 695 +
interfaces/ngs/Model.graphml | 801 +
interfaces/ngs/NOTES.txt | 9 +
interfaces/ngs/SimpleModel.graphml | 395 +
interfaces/ngs/cstdint | 1 +
interfaces/ngs/ncbi/NGS.hpp | 95 +
interfaces/os/linux/os-native.h | 43 +
interfaces/os/unix/oserror.h | 38 +
interfaces/os/unix/sysalloc.h | 40 +
interfaces/os/unix/unix-native.h | 58 +
interfaces/rdbms/rdbms.h | 362 +
interfaces/rdbms/sybase.h | 52 +
interfaces/search/extern.h | 41 +
interfaces/search/grep.h | 268 +
interfaces/search/nucstrstr.h | 153 +
interfaces/search/ref-variation.h | 159 +
interfaces/search/smith-waterman.h | 72 +
interfaces/simple/extern.h | 41 +
interfaces/simple/sra.hpp | 1127 +
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/generic-fastq.vschema | 265 +
interfaces/sra/helicos.vschema | 85 +
interfaces/sra/illumina.h | 170 +
interfaces/sra/illumina.vschema | 408 +
interfaces/sra/impl.h | 121 +
interfaces/sra/ion-torrent.vschema | 117 +
interfaces/sra/nanopore.vschema | 84 +
interfaces/sra/pacbio.h | 66 +
interfaces/sra/pacbio.vschema | 307 +
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/svdb/extern.h | 47 +
interfaces/svdb/svdb.h | 531 +
interfaces/tui/extern.h | 41 +
interfaces/tui/tui.h | 297 +
interfaces/tui/tui.hpp | 739 +
interfaces/tui/tui_dlg.h | 367 +
interfaces/vdb/blob.h | 154 +
interfaces/vdb/built-in.vschema | 412 +
interfaces/vdb/cursor.h | 490 +
interfaces/vdb/cursor.hpp | 388 +
interfaces/vdb/database.h | 334 +
interfaces/vdb/database.hpp | 347 +
interfaces/vdb/dependencies.h | 231 +
interfaces/vdb/extern.h | 47 +
interfaces/vdb/manager.h | 234 +
interfaces/vdb/manager.hpp | 386 +
interfaces/vdb/report.h | 92 +
interfaces/vdb/schema.h | 460 +
interfaces/vdb/schema.hpp | 252 +
interfaces/vdb/table.h | 424 +
interfaces/vdb/table.hpp | 328 +
interfaces/vdb/types.h | 39 +
interfaces/vdb/types.hpp | 230 +
interfaces/vdb/vdb-priv.h | 342 +
interfaces/vdb/vdb.h | 62 +
interfaces/vdb/vdb.vschema | 859 +
interfaces/vdb/xform.h | 826 +
interfaces/vfs/extern.h | 47 +
interfaces/vfs/keyring-priv.h | 52 +
interfaces/vfs/manager-priv.h | 161 +
interfaces/vfs/manager.h | 322 +
interfaces/vfs/path-priv.h | 266 +
interfaces/vfs/path.h | 294 +
interfaces/vfs/resolver.h | 311 +
interfaces/xfs/doc.h | 123 +
interfaces/xfs/editors.h | 310 +
interfaces/xfs/extern.h | 48 +
interfaces/xfs/handle.h | 106 +
interfaces/xfs/model.h | 248 +
interfaces/xfs/node.h | 217 +
interfaces/xfs/path.h | 227 +
interfaces/xfs/perm.h | 173 +
interfaces/xfs/tree.h | 176 +
interfaces/xfs/xfs-defs.h | 125 +
interfaces/xfs/xfs.h | 165 +
interfaces/xfs/xlog.h | 54 +
libs/Makefile | 89 +
libs/align/.gitignore | 1 +
libs/align/Makefile | 163 +
libs/align/al_iterator.c | 565 +
libs/align/align-access.c | 812 +
libs/align/align_mgr.c | 108 +
libs/align/bam-priv.h | 48 +
libs/align/bam.c | 5055 +++
libs/align/debug.h | 77 +
libs/align/dna-reverse-cmpl.c | 80 +
libs/align/pl_iterator.c | 689 +
libs/align/quality-quantizer.c | 109 +
libs/align/reader-cmn.c | 317 +
libs/align/reader-cmn.h | 81 +
libs/align/reader-refseq.c | 279 +
libs/align/reader-wgs.c | 169 +
libs/align/reader-wgs.h | 58 +
libs/align/ref_iterator.c | 863 +
libs/align/reference-cmn.c | 43 +
libs/align/reference-cmn.h | 38 +
libs/align/reference.c | 1943 ++
libs/align/refseq-mgr-priv.h | 35 +
libs/align/refseq-mgr.c | 1273 +
libs/align/writer-alignment.c | 440 +
libs/align/writer-cmn.c | 589 +
libs/align/writer-priv.h | 151 +
libs/align/writer-ref.c | 481 +
libs/align/writer-ref.h | 106 +
libs/align/writer-reference.c | 3186 ++
libs/align/writer-refseq.c | 179 +
libs/align/writer-sequence.c | 778 +
libs/ascp/Makefile | 87 +
libs/ascp/ascp-priv.h | 74 +
libs/ascp/ascp.c | 840 +
libs/ascp/linux/ascp-path.c | 119 +
libs/ascp/unix/connect.c | 618 +
libs/axf/.gitignore | 1 +
libs/axf/Makefile | 142 +
libs/axf/align-local_ref_id.c | 143 +
libs/axf/align-local_ref_start.c | 148 +
libs/axf/align-ref-name.c | 191 +
libs/axf/align-ref-pos.c | 299 +
libs/axf/align-ref-seq-id.c | 188 +
libs/axf/align-restore-read.c | 150 +
libs/axf/cigar.c | 2578 ++
libs/axf/generate-mismatch-qual.c | 152 +
libs/axf/get-sam-flags.c | 228 +
libs/axf/get_mate_align_ids.c | 332 +
libs/axf/make-cmp-read_desc.c | 176 +
libs/axf/mismatch-restore-qual.c | 135 +
libs/axf/not-my-row.c | 76 +
libs/axf/project_read_from_sequence.c | 285 +
libs/axf/raw-restore-qual.c | 95 +
libs/axf/raw-restore-read.c | 119 +
libs/axf/ref-preserve_qual.c | 429 +
libs/axf/ref-restore-read.c | 201 +
libs/axf/ref-tbl-sub-select.c | 533 +
libs/axf/ref-tbl.c | 106 +
libs/axf/ref-tbl.h | 32 +
libs/axf/refseq-stats.c | 205 +
libs/axf/seq-construct-read.c | 125 +
libs/axf/seq-restore-linkage-group.c | 186 +
libs/axf/seq-restore-read.c | 749 +
libs/axf/template-len.c | 136 +
libs/blast/Makefile | 91 +
libs/blast/blast-mgr.c | 670 +
libs/blast/blast-mgr.h | 78 +
libs/blast/reader.c | 2361 ++
libs/blast/reader.h | 53 +
libs/blast/reference.c | 1714 ++
libs/blast/reference.h | 86 +
libs/blast/run-set.c | 3251 ++
libs/blast/run-set.h | 313 +
libs/cipher/cipher-1.7/PKG-INFO | 13 +
libs/cipher/cipher-1.7/README.md | 4 +
libs/cipher/cipher-1.7/cipher.egg-info/PKG-INFO | 13 +
libs/cipher/cipher-1.7/cipher.egg-info/SOURCES.txt | 12 +
.../cipher.egg-info/dependency_links.txt | 1 +
.../cipher/cipher-1.7/cipher.egg-info/not-zip-safe | 1 +
.../cipher-1.7/cipher.egg-info/top_level.txt | 1 +
libs/cipher/cipher-1.7/cipher/__init__.py | 393 +
libs/cipher/cipher-1.7/decrypt.py | 25 +
libs/cipher/cipher-1.7/encrypt.py | 25 +
libs/cipher/cipher-1.7/requirements-test.txt | 5 +
libs/cipher/cipher-1.7/setup.cfg | 16 +
libs/cipher/cipher-1.7/setup.py | 4 +
libs/csra2/Makefile | 87 +
libs/hdf5/.gitignore | 2 +
libs/hdf5/Makefile | 122 +
libs/hdf5/hdf5arrayfile-priv.h | 79 +
libs/hdf5/hdf5arrayfile.c | 656 +
libs/hdf5/hdf5dir.c | 879 +
libs/hdf5/hdf5file.c | 383 +
libs/kapp/Makefile | 152 +
libs/kapp/args-conv.c | 43 +
libs/kapp/args.c | 2390 ++
libs/kapp/args_debug.h | 47 +
libs/kapp/linux/ram.c | 79 +
libs/kapp/loader-file.c | 643 +
libs/kapp/loader-meta.c | 105 +
libs/kapp/log-xml.c | 416 +
libs/kapp/main-priv.h | 76 +
libs/kapp/main.c | 516 +
libs/kapp/progressbar.c | 199 +
libs/kapp/queue-file.c | 925 +
libs/kapp/tokenizer.c | 525 +
libs/kapp/unix/args-conv-os.c | 32 +
libs/kapp/unix/sysmain.c | 296 +
.../htsjdk/samtools/apps => libs/kdb}/.gitignore | 0
libs/kdb/Makefile | 166 +
libs/kdb/btree.c | 579 +
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 | 122 +
libs/kdb/colidx.c | 243 +
libs/kdb/colidx0-priv.h | 93 +
libs/kdb/colidx0.c | 433 +
libs/kdb/colidx1-priv.h | 130 +
libs/kdb/colidx1.c | 771 +
libs/kdb/colidx2-priv.h | 99 +
libs/kdb/colidx2.c | 219 +
libs/kdb/column-cc.c | 229 +
libs/kdb/column-priv.h | 94 +
libs/kdb/column.c | 1132 +
libs/kdb/database-cc.c | 339 +
libs/kdb/database-cmn.c | 496 +
libs/kdb/database-priv.h | 115 +
libs/kdb/database.c | 807 +
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 | 951 +
libs/kdb/kdbfmt-priv.h | 76 +
libs/kdb/libkdb.vers.h | 27 +
libs/kdb/meta.c | 2141 ++
libs/kdb/ptrieval-v1.c | 265 +
libs/kdb/ptrieval-v2.c | 396 +
libs/kdb/rowset-it.c_old | 385 +
libs/kdb/rowset-priv.h_old | 116 +
libs/kdb/rowset-simple.c | 434 +
libs/kdb/rowset.c | 494 +
libs/kdb/rowset.c_old | 1513 +
libs/kdb/table-cc.c | 378 +
libs/kdb/table-priv.h | 81 +
libs/kdb/table.c | 721 +
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 | 166 +
libs/kdb/wcolidx.c | 694 +
libs/kdb/wcolidx0-priv.h | 153 +
libs/kdb/wcolidx0.c | 831 +
libs/kdb/wcolidx1-priv.h | 152 +
libs/kdb/wcolidx1.c | 921 +
libs/kdb/wcolidx2-priv.h | 114 +
libs/kdb/wcolidx2.c | 241 +
libs/kdb/wcolumn-priv.h | 120 +
libs/kdb/wcolumn.c | 2681 ++
libs/kdb/wdatabase-priv.h | 95 +
libs/kdb/wdatabase.c | 1642 +
libs/kdb/wdbmgr.c | 421 +
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 | 1430 +
libs/kdb/wmeta.c | 3526 +++
libs/kdb/wtable-priv.h | 106 +
libs/kdb/wtable.c | 1641 +
libs/kdb/wtrieidx-v1.c | 1100 +
libs/kdb/wtrieidx-v2.c | 2560 ++
libs/kdb/wu64idx-v3.c | 416 +
libs/kfc/Makefile | 97 +
libs/kfc/except.c | 128 +
libs/kfc/refcount.c | 181 +
libs/kfc/rsrc-priv.h | 44 +
libs/kfc/rsrc.c | 180 +
libs/kfc/sysctx-priv.h | 45 +
libs/kfc/tstate.c | 1041 +
libs/kfc/unix/sysctx.c | 192 +
libs/kfc/unix/sysrsrc.c | 148 +
libs/kfc/vtbl.c | 208 +
libs/kfc/xc.c | 36 +
libs/kfg/.gitignore | 2 +
libs/kfg/Makefile | 128 +
libs/kfg/certs.kfg | 31 +
libs/kfg/config-aws.c | 287 +
libs/kfg/config-grammar.c | 1726 ++
libs/kfg/config-grammar.y | 185 +
libs/kfg/config-lex.c | 2517 ++
libs/kfg/config-lex.l | 221 +
libs/kfg/config-tokens.h | 75 +
libs/kfg/config.c | 4387 +++
libs/kfg/default.kfg | 47 +
libs/kfg/kart.c | 720 +
libs/kfg/keystore.c | 858 +
libs/kfg/kfg-lex.h | 67 +
libs/kfg/kfg-parse.h | 41 +
libs/kfg/kfg-priv.h | 32 +
libs/kfg/ngc-priv.h | 59 +
libs/kfg/ngc.c | 484 +
libs/kfg/properties.c | 768 +
libs/kfg/report-kfg.c | 532 +
libs/kfg/repository.c | 1982 ++
libs/kfs/.gitignore | 1 +
libs/kfs/Makefile | 221 +
libs/kfs/arc.c | 4089 +++
libs/kfs/arrayfile.c | 423 +
libs/kfs/buffile-read.c | 265 +
libs/kfs/buffile-write.c | 371 +
libs/kfs/buffile.c | 574 +
libs/kfs/bzip.c | 836 +
libs/kfs/cacheteefile.c | 1833 ++
libs/kfs/countfile.c | 652 +
libs/kfs/crc32.c | 1771 ++
libs/kfs/dir_test.c | 54 +
libs/kfs/directory-v2.c | 1185 +
libs/kfs/directory.c | 1539 +
libs/kfs/extendable-ramfile.c | 280 +
libs/kfs/ffext.c | 812 +
libs/kfs/ffkey.c | 833 +
libs/kfs/ffmagic.c | 969 +
libs/kfs/file-v2.c | 724 +
libs/kfs/file.c | 1002 +
libs/kfs/fileformat-priv.h | 124 +
libs/kfs/fileformat.c | 291 +
libs/kfs/from_to_namelist.c | 454 +
libs/kfs/gzip.c | 646 +
libs/kfs/impl.h | 120 +
libs/kfs/karc-priv.h | 43 +
libs/kfs/kfs-priv.h | 47 +
libs/kfs/kfsmagic | 20101 ++++++++++++
libs/kfs/lockfile.c | 350 +
libs/kfs/manager.c | 641 +
libs/kfs/md5.c | 1910 ++
libs/kfs/mmap-priv.h | 111 +
libs/kfs/mmap.c | 754 +
libs/kfs/nullfile.c | 273 +
libs/kfs/pagefile.c | 1388 +
libs/kfs/pmem.c | 632 +
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/szip.c | 575 +
libs/kfs/tar.c | 2684 ++
libs/kfs/teefile.c | 532 +
libs/kfs/toc-priv.h | 841 +
libs/kfs/toc.c | 1764 ++
libs/kfs/tocdir.c | 411 +
libs/kfs/tocentry.c | 1748 ++
libs/kfs/tocfile.c | 635 +
libs/kfs/unix/sysdir-priv.h | 68 +
libs/kfs/unix/sysdir.c | 2414 ++
libs/kfs/unix/sysdll.c | 1436 +
libs/kfs/unix/sysfile-priv.h | 89 +
libs/kfs/unix/sysfile-v2.c | 1018 +
libs/kfs/unix/sysfile.c | 1079 +
libs/kfs/unix/syslockfile.c | 215 +
libs/kfs/unix/sysmmap-priv.h | 68 +
libs/kfs/unix/sysmmap.c | 143 +
libs/klib/.gitignore | 1 +
libs/klib/Judy.h | 635 +
libs/klib/Makefile | 159 +
libs/klib/SHA-32bit.c | 313 +
libs/klib/SHA-64bit.c | 271 +
libs/klib/bsd/syserrcode.c | 44 +
libs/klib/bsearch.c | 77 +
libs/klib/bstpersist.c | 252 +
libs/klib/btree.c | 1457 +
libs/klib/container.c | 1646 +
libs/klib/cp1252.c | 65 +
libs/klib/crc32.c | 500 +
libs/klib/data-buffer.c | 656 +
libs/klib/debug.c | 352 +
libs/klib/iso8859-1.c | 42 +
libs/klib/iso8859.c | 205 +
libs/klib/judy-vector.c | 1793 ++
.../samtools/fastq => libs/klib/judy}/.gitignore | 0
libs/klib/judy/Judy1.h | 549 +
libs/klib/judy/Judy1Tables.32.c | 72 +
libs/klib/judy/Judy1Tables.64.c | 132 +
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/JudyLTables.32.c | 121 +
libs/klib/judy/JudyLTables.64.c | 219 +
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/Judy_Bit.c | 23 +
libs/klib/judy/Judy_Bit_Cascade.c | 3 +
libs/klib/judy/Judy_Bit_Count.c | 3 +
libs/klib/judy/Judy_Bit_Decascade.c | 3 +
libs/klib/judy/Judy_Bit_Next.c | 3 +
libs/klib/judy/Judy_Bit_NextEmpty.c | 3 +
libs/klib/judy/Judy_Bit_Prev.c | 3 +
libs/klib/judy/Judy_Word.c | 23 +
libs/klib/judy/Judy_Word_Cascade.c | 3 +
libs/klib/judy/Judy_Word_Count.c | 3 +
libs/klib/judy/Judy_Word_Decascade.c | 3 +
libs/klib/judy/Judy_Word_Next.c | 3 +
libs/klib/judy/Judy_Word_NextEmpty.c | 3 +
libs/klib/judy/Judy_Word_Prev.c | 3 +
libs/klib/judy/Makefile | 225 +
libs/klib/judy/_Judy1Tables.c | 31 +
libs/klib/judy/_JudyLTables.c | 31 +
libs/klib/judy/j__udyGet.c | 2 +
libs/klib/ksort.c | 98 +
libs/klib/linux/syserrcode.c | 53 +
libs/klib/log-priv.h | 96 +
libs/klib/log.c | 986 +
libs/klib/maybeswap.h | 57 +
libs/klib/md5.c | 421 +
libs/klib/namelist.c | 149 +
libs/klib/ncbi-vdb-version.c | 45 +
libs/klib/num-gen.c | 1157 +
libs/klib/out.c | 208 +
libs/klib/pack.c | 517 +
libs/klib/pbstree-impl.c | 847 +
libs/klib/pbstree-native.c | 30 +
libs/klib/pbstree-priv.h | 680 +
libs/klib/pbstree-swapped.c | 30 +
libs/klib/pbstree.c | 395 +
libs/klib/printf.c | 3540 +++
libs/klib/progressbar.c | 160 +
libs/klib/ptpersist.c | 1121 +
libs/klib/ptrie.c | 1992 ++
libs/klib/qsort.c | 311 +
libs/klib/rc-idx-tbl.c | 41 +
libs/klib/rc-tbl.c | 38 +
libs/klib/refcount.c | 499 +
libs/klib/release-vers.h | 44 +
libs/klib/report-klib.c | 912 +
libs/klib/sra-release-version.c | 335 +
libs/klib/status-rc-strings.c | 40 +
libs/klib/status-rc.c | 156 +
libs/klib/status.c | 439 +
libs/klib/symtab.c | 736 +
libs/klib/text.c | 1134 +
libs/klib/time.c | 3 +
libs/klib/token.c | 1291 +
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 | 162 +
libs/klib/unix/syswriter.c | 163 +
libs/klib/unpack.c | 833 +
libs/klib/utf8.c | 1355 +
libs/klib/vector.c | 626 +
libs/klib/vector_namelist.c | 633 +
libs/klib/vlen-encode.c | 773 +
libs/klib/writer-priv.h | 169 +
libs/klib/writer.c | 645 +
libs/kns/Makefile | 116 +
libs/kns/buffered-stream.c | 249 +
libs/kns/endpoint.c | 155 +
libs/kns/http-client.c | 3575 +++
libs/kns/http-file.c | 638 +
libs/kns/http-priv.h | 132 +
libs/kns/http-retrier.c | 503 +
libs/kns/http.c | 341 +
libs/kns/kns_manager-ext.c | 157 +
libs/kns/kns_manager.c | 346 +
libs/kns/linux/sysendpoint.c | 158 +
libs/kns/linux/syspoll.c | 107 +
libs/kns/manager.c | 1033 +
libs/kns/mgr-priv.h | 92 +
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 | 52 +
libs/kns/stream.c | 782 +
libs/kns/sysmgr.h | 41 +
libs/kns/tls-priv.h | 80 +
libs/kns/tls.c | 1087 +
libs/kns/unix/sysmgr.c | 37 +
libs/kns/unix/syssock.c | 1435 +
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/kproc/Makefile | 162 +
libs/kproc/bsd/syslock-priv.h | 72 +
libs/kproc/bsd/syslock.c | 932 +
libs/kproc/bsd/sysmgr.c | 38 +
libs/kproc/linux/sysbarrier.c | 170 +
libs/kproc/linux/syslock-priv.h | 68 +
libs/kproc/linux/syslock.c | 617 +
libs/kproc/linux/sysmgr.c | 52 +
libs/kproc/procmgr.c | 445 +
libs/kproc/queue.c | 428 +
libs/kproc/sem.c | 472 +
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 | 128 +
libs/krypto/.gitignore | 2 +
libs/krypto/Makefile | 297 +
libs/krypto/aes-byte.c | 236 +
libs/krypto/aes-impl.c | 1 +
libs/krypto/aes-ncbi-ni.c | 2 +
libs/krypto/aes-ncbi-priv.h | 227 +
libs/krypto/aes-ncbi.c | 2641 ++
libs/krypto/aes-priv.h | 94 +
libs/krypto/aes.c | 1 +
libs/krypto/aes_core.c | 1181 +
libs/krypto/aes_x86core.c | 2 +
libs/krypto/aesx86.c | 1 +
libs/krypto/blockcipher-byte-impl.h | 113 +
libs/krypto/blockcipher-impl.h | 187 +
libs/krypto/blockcipher-priv.h | 90 +
libs/krypto/blockcipher-vec-impl.h | 119 +
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 | 543 +
libs/krypto/ciphermgr.c | 295 +
libs/krypto/ciphertest.c | 80 +
libs/krypto/compile-test.c | 50 +
libs/krypto/csprng.c | 163 +
libs/krypto/encfile-priv.h | 162 +
libs/krypto/encfile.c | 2019 ++
libs/krypto/encfilev2.c | 2622 ++
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 | 1243 +
libs/krypto/rng-impl.h | 91 +
.../source/.gitignore => libs/krypto/rng-priv.h | 0
libs/krypto/rng.c | 120 +
libs/krypto/testcipher.c | 76 +
libs/krypto/unix/sysrng.c | 114 +
libs/krypto/wgaencrypt.c | 1254 +
libs/ktst/Makefile | 87 +
libs/ktst/testcase.cpp | 108 +
libs/ktst/testenv.cpp | 518 +
libs/ktst/testrunner.cpp | 86 +
libs/ktst/unix/systestenv.cpp | 137 +
libs/kxml/Makefile | 117 +
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 | 88 +
libs/loader/alignment-writer.c | 271 +
libs/loader/common-reader.c | 614 +
libs/loader/common-writer.c | 2067 ++
libs/loader/mmarray.c | 131 +
libs/loader/reference-writer.c | 483 +
libs/loader/sequence-writer.c | 366 +
libs/ncbi-vdb/Makefile | 160 +
libs/ncbi-vdb/libncbi-vdb.vers | 1 +
libs/ngs-c++/Makefile | 103 +
libs/ngs-c++/NCBI-NGS.cpp | 106 +
libs/ngs-c++/testy-the-bear.cpp | 277 +
libs/ngs-jni/.gitignore | 1 +
libs/ngs-jni/Makefile | 109 +
libs/ngs-jni/jni_ErrorMsg.c | 173 +
libs/ngs-jni/jni_ErrorMsg.h | 89 +
libs/ngs-jni/jni_Manager.c | 250 +
libs/ngs-jni/jni_Manager.h | 77 +
libs/ngs-jni/jni_String.c | 195 +
libs/ngs-jni/jni_String.h | 91 +
libs/ngs-py/Makefile | 87 +
libs/ngs-py/py_Manager.c | 218 +
libs/ngs-py/py_Manager.h | 27 +
libs/ngs-py/py_ngs_defs.h | 15 +
libs/ngs/BAM_Alignment.c | 657 +
libs/ngs/BAM_Alignment.h | 58 +
libs/ngs/BAM_ReadCollection.c | 1522 +
libs/ngs/BAM_Record.c | 142 +
libs/ngs/BAM_Record.h | 82 +
libs/ngs/CSRA1_Alignment.c | 1451 +
libs/ngs/CSRA1_Alignment.h | 83 +
libs/ngs/CSRA1_Pileup.c | 1921 ++
libs/ngs/CSRA1_Pileup.h | 341 +
libs/ngs/CSRA1_PileupEvent.c | 931 +
libs/ngs/CSRA1_PileupEvent.h | 50 +
libs/ngs/CSRA1_Read.c | 463 +
libs/ngs/CSRA1_Read.h | 96 +
libs/ngs/CSRA1_ReadCollection.c | 753 +
libs/ngs/CSRA1_ReadCollection.h | 58 +
libs/ngs/CSRA1_Reference.c | 1102 +
libs/ngs/CSRA1_Reference.h | 96 +
libs/ngs/CSRA1_ReferenceWindow.c | 1062 +
libs/ngs/CSRA1_ReferenceWindow.h | 67 +
libs/ngs/EBI_ReferenceSequence.c | 402 +
libs/ngs/EBI_ReferenceSequence.h | 51 +
libs/ngs/Makefile | 129 +
libs/ngs/Model.graphml | 661 +
libs/ngs/NCBI-NGS.c | 66 +
libs/ngs/NCBI-NGS.h | 58 +
libs/ngs/NGS_Alignment.c | 993 +
libs/ngs/NGS_Alignment.h | 209 +
libs/ngs/NGS_Cursor.c | 611 +
libs/ngs/NGS_Cursor.h | 140 +
libs/ngs/NGS_ErrBlock.c | 57 +
libs/ngs/NGS_ErrBlock.h | 53 +
libs/ngs/NGS_Fragment.c | 286 +
libs/ngs/NGS_Fragment.h | 175 +
libs/ngs/NGS_FragmentBlob.c | 414 +
libs/ngs/NGS_FragmentBlob.h | 125 +
libs/ngs/NGS_FragmentBlobIterator.c | 185 +
libs/ngs/NGS_FragmentBlobIterator.h | 79 +
libs/ngs/NGS_Id.c | 179 +
libs/ngs/NGS_Id.h | 93 +
libs/ngs/NGS_Pileup.c | 235 +
libs/ngs/NGS_Pileup.h | 147 +
libs/ngs/NGS_PileupEvent.c | 493 +
libs/ngs/NGS_PileupEvent.h | 179 +
libs/ngs/NGS_Read.c | 522 +
libs/ngs/NGS_Read.h | 190 +
libs/ngs/NGS_ReadCollection.c | 674 +
libs/ngs/NGS_ReadCollection.h | 194 +
libs/ngs/NGS_ReadGroup.c | 229 +
libs/ngs/NGS_ReadGroup.h | 127 +
libs/ngs/NGS_Refcount.c | 182 +
libs/ngs/NGS_Refcount.h | 102 +
libs/ngs/NGS_Reference.c | 916 +
libs/ngs/NGS_Reference.h | 214 +
libs/ngs/NGS_ReferenceSequence.c | 282 +
libs/ngs/NGS_ReferenceSequence.h | 138 +
libs/ngs/NGS_Statistics.c | 336 +
libs/ngs/NGS_Statistics.h | 143 +
libs/ngs/NGS_String.c | 413 +
libs/ngs/NGS_String.h | 109 +
libs/ngs/NOTES.txt | 128 +
libs/ngs/SRA_DB_ReadCollection.c | 456 +
libs/ngs/SRA_Read.c | 943 +
libs/ngs/SRA_Read.h | 173 +
libs/ngs/SRA_ReadCollection.c | 424 +
libs/ngs/SRA_ReadGroup.c | 429 +
libs/ngs/SRA_ReadGroup.h | 73 +
libs/ngs/SRA_ReadGroupInfo.c | 333 +
libs/ngs/SRA_ReadGroupInfo.h | 89 +
libs/ngs/SRA_ReferenceSequence.c | 374 +
libs/ngs/SRA_ReferenceSequence.h | 56 +
libs/ngs/SRA_Statistics.c | 792 +
libs/ngs/SRA_Statistics.h | 61 +
libs/ngs/VByteBlob.c | 117 +
libs/ngs/VByteBlob.h | 47 +
libs/ngs/extern.h | 41 +
.../htsjdk/tribble/tmp => libs/search}/.gitignore | 0
libs/search/Makefile | 98 +
libs/search/agrep-dp.c | 880 +
libs/search/agrep-myers.c | 644 +
libs/search/agrep-myersunltd.c | 1039 +
libs/search/agrep-wumanber.c | 415 +
libs/search/debug.h | 43 +
libs/search/fgrep-aho.c | 363 +
libs/search/fgrep-boyermoore.c | 462 +
libs/search/fgrep-dumb.c | 326 +
libs/search/nucstrstr.c | 4621 +++
libs/search/search-priv.h | 140 +
libs/search/search.c | 388 +
libs/search/sw-search.c | 1496 +
libs/sra/.gitignore | 1 +
libs/sra/Makefile | 249 +
libs/sra/built-in.vschema | 580 +
libs/sra/libsra-schema.vers.h | 27 +
libs/sra/libsradb.vers.h | 27 +
libs/sra/libsrareader.vers.h | 1 +
libs/sra/libsraschema.vers.h | 1 +
libs/sra/libwsradb.vers.h | 1 +
libs/sra/libwsraschema.vers.h | 1 +
libs/sra/reader-abi.c | 473 +
libs/sra/reader-cmn.c | 379 +
libs/sra/reader-cmn.h | 161 +
libs/sra/reader-fastq.c | 623 +
libs/sra/reader-illumina.c | 567 +
libs/sra/reader-sff.c | 380 +
libs/sra/sra-debug.h | 42 +
libs/sra/sra-dflt-schema.c | 552 +
libs/sra/sra-priv.h | 183 +
libs/sra/sra-schema.c | 4133 +++
libs/sra/sracache.c | 560 +
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 | 1458 +
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/.gitignore | 1 +
libs/sraxf/Makefile | 152 +
libs/sraxf/bio-start.c | 197 +
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 | 354 +
libs/sraxf/extract-name_coord.c | 243 +
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 | 333 +
libs/sraxf/fpcodec.c | 267 +
libs/sraxf/index_lookup.c | 270 +
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/qstat-trigger.c | 256 +
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 | 223 +
libs/sraxf/rotate.c | 271 +
libs/sraxf/spot-desc.c | 102 +
libs/sraxf/stat_mod.c | 392 +
libs/sraxf/stat_mod.h | 80 +
libs/sraxf/stats.c | 764 +
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 | 146 +
libs/sraxf/tokenize-spot_name-generic-fastq.c | 81 +
libs/sraxf/tokenize-spot_name-helicos.c | 112 +
libs/sraxf/tokenize-spot_name-illumina.c | 151 +
libs/sraxf/tokenize-spot_name-ion-torrent.c | 136 +
libs/sraxf/untyped-priv.h | 83 +
libs/sraxf/untyped.c | 378 +
libs/sraxf/v0-decompress-init.c | 2838 ++
libs/sraxf/v0-decompress-local.h | 368 +
libs/sraxf/v0-decompress.c | 1093 +
libs/sraxf/v0-decompress.h | 170 +
libs/sraxf/v0-funcs.c | 337 +
libs/sraxf/varloc.c | 105 +
libs/svdb/.gitignore | 1 +
libs/svdb/Makefile | 95 +
libs/svdb/svdb.c | 3215 ++
libs/tui/Makefile | 137 +
libs/tui/bsd/systui.c | 619 +
libs/tui/dir_dlg.c | 470 +
libs/tui/eventring.c | 134 +
libs/tui/eventring.h | 74 +
libs/tui/file_dlg.c | 380 +
libs/tui/line_policy.c | 379 +
libs/tui/line_policy.h | 86 +
libs/tui/linux/systui.c | 624 +
libs/tui/screen.c | 209 +
libs/tui/screen.h | 75 +
libs/tui/string_cache.c | 378 +
libs/tui/string_cache.h | 54 +
libs/tui/tui-priv.h | 87 +
libs/tui/tui.c | 380 +
libs/tui/tui_cpp.cpp | 226 +
libs/tui/tui_dlg.c | 1291 +
libs/tui/tui_dlg_helper.c | 250 +
libs/tui/tui_menu.c | 913 +
libs/tui/tui_menu.h | 49 +
libs/tui/tui_palette.c | 304 +
libs/tui/tui_std_dlg.c | 355 +
libs/tui/tui_widget.c | 1079 +
libs/tui/tui_widget.h | 210 +
libs/tui/tui_widget_button.c | 87 +
libs/tui/tui_widget_checkbox.c | 87 +
libs/tui/tui_widget_grid.c | 488 +
libs/tui/tui_widget_inputline.c | 181 +
libs/tui/tui_widget_label.c | 53 +
libs/tui/tui_widget_progress.c | 120 +
libs/tui/tui_widget_radiobox.c | 130 +
libs/tui/tui_widget_spin_edit.c | 118 +
libs/tui/tui_widget_string_list.c | 183 +
libs/tui/unix/systui.c | 29 +
libs/vdb/.gitignore | 1 +
libs/vdb/Makefile | 188 +
libs/vdb/blob-headers.c | 726 +
libs/vdb/blob-headers.h | 114 +
libs/vdb/blob-priv.h | 206 +
libs/vdb/blob.c | 1690 +
libs/vdb/blob.h | 84 +
libs/vdb/cast.c | 583 +
libs/vdb/column-cmn.c | 356 +
libs/vdb/column-priv.h | 304 +
libs/vdb/column.c | 80 +
libs/vdb/compare.c | 242 +
libs/vdb/cursor-cmn.c | 2910 ++
libs/vdb/cursor-priv.h | 322 +
libs/vdb/cursor.c | 200 +
libs/vdb/database-cmn.c | 928 +
libs/vdb/database-depend.c | 1807 ++
libs/vdb/database-load.c | 119 +
libs/vdb/database-priv.h | 150 +
libs/vdb/database.c | 29 +
libs/vdb/dbmgr-cmn.c | 943 +
libs/vdb/dbmgr-priv.h | 115 +
libs/vdb/dbmgr.c | 157 +
libs/vdb/delta_average.c | 298 +
libs/vdb/environment-read.c | 108 +
libs/vdb/fixed-row-len.c | 67 +
libs/vdb/gen-cast.pl | 480 +
libs/vdb/index_insert.c | 150 +
libs/vdb/index_lookup.c | 191 +
libs/vdb/index_project.c | 221 +
libs/vdb/libvdb.vers.h | 27 +
libs/vdb/linker-cmn.c | 656 +
libs/vdb/linker-int.c | 679 +
libs/vdb/linker-priv.h | 272 +
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 | 1734 ++
libs/vdb/page-map.h | 386 +
libs/vdb/parameter-read.c | 103 +
libs/vdb/phys-cmn.c | 784 +
libs/vdb/phys-load.c | 330 +
libs/vdb/phys-priv.h | 194 +
libs/vdb/phys.c | 67 +
libs/vdb/prod-cmn.c | 2567 ++
libs/vdb/prod-expr.c | 885 +
libs/vdb/prod-expr.h | 202 +
libs/vdb/prod-func.c | 957 +
libs/vdb/prod-priv.h | 462 +
libs/vdb/prod.c | 136 +
libs/vdb/range-validate.c | 195 +
libs/vdb/redimension.c | 108 +
libs/vdb/report-vdb.c | 853 +
libs/vdb/row-id.c | 64 +
libs/vdb/row-len.c | 65 +
libs/vdb/schema-db.c | 752 +
libs/vdb/schema-dump.c | 683 +
libs/vdb/schema-dump.h | 208 +
libs/vdb/schema-eval.c | 1400 +
libs/vdb/schema-expr.c | 2170 ++
libs/vdb/schema-expr.h | 396 +
libs/vdb/schema-func.c | 1658 +
libs/vdb/schema-int.c | 376 +
libs/vdb/schema-parse.c | 857 +
libs/vdb/schema-parse.h | 607 +
libs/vdb/schema-priv.h | 1308 +
libs/vdb/schema-prod.c | 1005 +
libs/vdb/schema-tbl.c | 2925 ++
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 | 1401 +
libs/vdb/table-load.c | 323 +
libs/vdb/table-priv.h | 238 +
libs/vdb/table.c | 109 +
libs/vdb/test/Makefile | 51 +
libs/vdb/test/test-prod-cmn.c | 10 +
libs/vdb/transpose.c | 720 +
libs/vdb/wcolumn.c | 1074 +
libs/vdb/wcursor.c | 1238 +
libs/vdb/wdatabase.c | 680 +
libs/vdb/wdbmgr.c | 267 +
libs/vdb/wlinker.c | 98 +
libs/vdb/wphys.c | 912 +
libs/vdb/wprod.c | 439 +
libs/vdb/wtable.c | 1055 +
libs/vdb/xform-priv.h | 83 +
libs/vfs/Makefile | 102 +
libs/vfs/keyring.c | 292 +
libs/vfs/keyring.h | 111 +
libs/vfs/kurl-stub.c | 18 +
libs/vfs/manager.c | 3519 +++
libs/vfs/path-priv.h | 148 +
libs/vfs/path.c | 3801 +++
libs/vfs/resolver-3.0.c | 326 +
libs/vfs/resolver-priv.h | 244 +
libs/vfs/resolver.c | 4876 +++
libs/vfs/srapath-stub.c | 372 +
libs/vfs/srapath.c | 1424 +
libs/vfs/unix/syskeyring.c | 161 +
libs/vfs/unix/syspath.c | 155 +
libs/vxf/.gitignore | 1 +
libs/vxf/Makefile | 196 +
libs/vxf/add-row-id.c | 80 +
libs/vxf/bit_or.c | 135 +
libs/vxf/bunzip.c | 130 +
libs/vxf/bzip.c | 184 +
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 | 109 +
libs/vxf/diff.c | 356 +
libs/vxf/echo.c | 187 +
libs/vxf/entrez.c | 170 +
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 | 113 +
libs/vxf/integral_0.c | 114 +
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 | 866 +
libs/vxf/lower-case-tech-reads.c | 111 +
libs/vxf/map.c | 1017 +
libs/vxf/math-funcs-impl.h | 361 +
libs/vxf/max.c | 175 +
libs/vxf/min.c | 175 +
libs/vxf/outlier-decoder.c | 113 +
libs/vxf/outlier-encoder.c | 141 +
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 | 293 +
libs/vxf/sprintf.c | 1280 +
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 | 213 +
libs/vxf/zip.c | 216 +
libs/wgsxf/Makefile | 127 +
libs/wgsxf/build_read_type.c | 113 +
libs/wgsxf/build_scaffold.c | 435 +
libs/xfs/Makefile | 140 +
libs/xfs/bogus.c | 373 +
libs/xfs/common.h | 217 +
libs/xfs/contnode.c | 685 +
libs/xfs/contnode.h | 98 +
libs/xfs/doc.c | 730 +
libs/xfs/docnode.c | 745 +
libs/xfs/editors.c | 491 +
libs/xfs/encro.c | 875 +
libs/xfs/encws.c | 1793 ++
libs/xfs/foo.c | 250 +
libs/xfs/gap.c | 585 +
libs/xfs/gapc.c | 993 +
libs/xfs/gapf.c | 879 +
libs/xfs/gapk.c | 440 +
libs/xfs/gapka.c | 1005 +
libs/xfs/gapks.c | 882 +
libs/xfs/handle.c | 227 +
libs/xfs/http.c | 1300 +
libs/xfs/kfs.c | 2038 ++
libs/xfs/lockdpt.c | 192 +
libs/xfs/lockdpt.h | 76 +
libs/xfs/lreader.c | 459 +
libs/xfs/lreader.h | 117 +
libs/xfs/mehr.c | 258 +
libs/xfs/mehr.h | 77 +
libs/xfs/model.c | 1157 +
libs/xfs/ncon.c | 525 +
libs/xfs/ncon.h | 98 +
libs/xfs/node.c | 616 +
libs/xfs/owp.c | 375 +
libs/xfs/owp.h | 86 +
libs/xfs/path.c | 1505 +
libs/xfs/perm.c | 805 +
libs/xfs/platform.h | 51 +
libs/xfs/readme.c | 193 +
libs/xfs/schwarzschraube.c | 334 +
libs/xfs/schwarzschraube.h | 118 +
libs/xfs/simcon.c | 214 +
libs/xfs/spen.c | 963 +
libs/xfs/spen.h | 121 +
libs/xfs/tar.c | 1225 +
libs/xfs/teleport.c | 460 +
libs/xfs/teleport.h | 108 +
libs/xfs/tree.c | 717 +
libs/xfs/unix/operations.c | 2155 ++
libs/xfs/unix/operations.h | 54 +
libs/xfs/unix/platform.c | 359 +
libs/xfs/unix/security.c | 24 +
libs/xfs/xencro.c | 944 +
libs/xfs/xencro.h | 118 +
libs/xfs/xencws.c | 5090 +++
libs/xfs/xencws.h | 71 +
libs/xfs/xfs-priv.h | 118 +
libs/xfs/xfs.c | 403 +
libs/xfs/xgap.c | 1408 +
libs/xfs/xgap.h | 244 +
libs/xfs/xgapf.c | 1822 ++
libs/xfs/xgapf.h | 126 +
libs/xfs/xgapk.c | 1777 ++
libs/xfs/xgapk.h | 184 +
libs/xfs/xhttp.c | 2988 ++
libs/xfs/xhttp.h | 174 +
libs/xfs/xlog.c | 295 +
libs/xfs/xtar.c | 1248 +
libs/xfs/xtar.h | 160 +
libs/xfs/zehr.c | 1063 +
libs/xfs/zehr.h | 266 +
local-builds.sh | 72 +
schema_crc.pl | 148 +
scripts/explain_sam_flags.py | 65 -
scripts/release_picard.sh | 152 -
setup/install | 45 +
setup/install.perl | 1329 +
setup/install.prl | 9 +
setup/konfigure.perl | 1762 ++
setup/os-arch.perl | 22 +
setup/os-arch.prl | 106 +
setup/package.prl | 57 +
setup/s/install | 45 +
setup/s/os.prl | 2 +
.../java/htsjdk/samtools/AbstractBAMFileIndex.java | 721 -
.../htsjdk/samtools/AbstractSAMHeaderRecord.java | 116 -
src/main/java/htsjdk/samtools/AlignmentBlock.java | 58 -
.../java/htsjdk/samtools/AsyncSAMFileWriter.java | 59 -
.../java/htsjdk/samtools/BAMFileConstants.java | 45 -
src/main/java/htsjdk/samtools/BAMFileReader.java | 913 -
src/main/java/htsjdk/samtools/BAMFileSpan.java | 268 -
src/main/java/htsjdk/samtools/BAMFileWriter.java | 200 -
src/main/java/htsjdk/samtools/BAMIndex.java | 67 -
src/main/java/htsjdk/samtools/BAMIndexContent.java | 69 -
.../java/htsjdk/samtools/BAMIndexMetaData.java | 271 -
src/main/java/htsjdk/samtools/BAMIndexWriter.java | 54 -
src/main/java/htsjdk/samtools/BAMIndexer.java | 313 -
.../java/htsjdk/samtools/BAMIteratorFilter.java | 26 -
.../BAMQueryMultipleIntervalsIteratorFilter.java | 59 -
src/main/java/htsjdk/samtools/BAMRecord.java | 365 -
src/main/java/htsjdk/samtools/BAMRecordCodec.java | 210 -
src/main/java/htsjdk/samtools/BamFileIoUtils.java | 178 -
.../java/htsjdk/samtools/BamIndexValidator.java | 151 -
src/main/java/htsjdk/samtools/Bin.java | 162 -
src/main/java/htsjdk/samtools/BinList.java | 119 -
.../java/htsjdk/samtools/BinaryBAMIndexWriter.java | 207 -
.../java/htsjdk/samtools/BinaryCigarCodec.java | 89 -
src/main/java/htsjdk/samtools/BinaryTagCodec.java | 425 -
.../java/htsjdk/samtools/BinningIndexBuilder.java | 187 -
.../java/htsjdk/samtools/BinningIndexContent.java | 263 -
.../java/htsjdk/samtools/BrowseableBAMIndex.java | 54 -
src/main/java/htsjdk/samtools/CRAMBAIIndexer.java | 474 -
src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java | 135 -
.../htsjdk/samtools/CRAMContainerStreamWriter.java | 495 -
src/main/java/htsjdk/samtools/CRAMFileReader.java | 559 -
src/main/java/htsjdk/samtools/CRAMFileWriter.java | 168 -
src/main/java/htsjdk/samtools/CRAMIterator.java | 310 -
.../java/htsjdk/samtools/CachingBAMFileIndex.java | 169 -
.../samtools/ChainedDownsamplingIterator.java | 90 -
src/main/java/htsjdk/samtools/Chunk.java | 169 -
src/main/java/htsjdk/samtools/Cigar.java | 340 -
src/main/java/htsjdk/samtools/CigarElement.java | 75 -
src/main/java/htsjdk/samtools/CigarOperator.java | 211 -
.../samtools/ComparableSamRecordIterator.java | 89 -
.../ConstantMemoryDownsamplingIterator.java | 88 -
.../samtools/CoordinateSortedPairInfoMap.java | 297 -
.../java/htsjdk/samtools/CustomReaderFactory.java | 143 -
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 54 -
src/main/java/htsjdk/samtools/Defaults.java | 174 -
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 78 -
.../java/htsjdk/samtools/DownsamplingIterator.java | 113 -
.../samtools/DownsamplingIteratorFactory.java | 118 -
.../htsjdk/samtools/DuplicateScoringStrategy.java | 138 -
src/main/java/htsjdk/samtools/DuplicateSet.java | 184 -
.../java/htsjdk/samtools/DuplicateSetIterator.java | 172 -
.../htsjdk/samtools/FileTruncatedException.java | 46 -
src/main/java/htsjdk/samtools/FixBAMFile.java | 46 -
.../java/htsjdk/samtools/GenomicIndexUtil.java | 100 -
.../samtools/HighAccuracyDownsamplingIterator.java | 196 -
src/main/java/htsjdk/samtools/LinearIndex.java | 126 -
.../htsjdk/samtools/MergingSamRecordIterator.java | 238 -
.../samtools/NotPrimarySkippingIterator.java | 62 -
src/main/java/htsjdk/samtools/QueryInterval.java | 96 -
.../java/htsjdk/samtools/ReservedTagConstants.java | 70 -
.../SAMBinaryTagAndUnsignedArrayValue.java | 65 -
.../java/htsjdk/samtools/SAMBinaryTagAndValue.java | 251 -
src/main/java/htsjdk/samtools/SAMException.java | 44 -
src/main/java/htsjdk/samtools/SAMFileHeader.java | 399 -
src/main/java/htsjdk/samtools/SAMFileSource.java | 68 -
src/main/java/htsjdk/samtools/SAMFileSpan.java | 49 -
src/main/java/htsjdk/samtools/SAMFileWriter.java | 50 -
.../java/htsjdk/samtools/SAMFileWriterFactory.java | 505 -
.../java/htsjdk/samtools/SAMFileWriterImpl.java | 247 -
src/main/java/htsjdk/samtools/SAMFlag.java | 110 -
.../java/htsjdk/samtools/SAMFormatException.java | 44 -
.../htsjdk/samtools/SAMHeaderRecordComparator.java | 68 -
src/main/java/htsjdk/samtools/SAMLineParser.java | 487 -
.../java/htsjdk/samtools/SAMProgramRecord.java | 132 -
.../java/htsjdk/samtools/SAMReadGroupRecord.java | 165 -
src/main/java/htsjdk/samtools/SAMRecord.java | 2378 --
.../java/htsjdk/samtools/SAMRecordComparator.java | 40 -
.../samtools/SAMRecordCoordinateComparator.java | 105 -
.../samtools/SAMRecordDuplicateComparator.java | 363 -
.../java/htsjdk/samtools/SAMRecordFactory.java | 28 -
.../java/htsjdk/samtools/SAMRecordIterator.java | 52 -
.../samtools/SAMRecordQueryHashComparator.java | 72 -
.../samtools/SAMRecordQueryNameComparator.java | 89 -
.../java/htsjdk/samtools/SAMRecordSetBuilder.java | 576 -
src/main/java/htsjdk/samtools/SAMRecordUtil.java | 77 -
.../htsjdk/samtools/SAMSequenceDictionary.java | 355 -
.../samtools/SAMSequenceDictionaryCodec.java | 114 -
.../java/htsjdk/samtools/SAMSequenceRecord.java | 248 -
.../java/htsjdk/samtools/SAMSortOrderChecker.java | 89 -
src/main/java/htsjdk/samtools/SAMTag.java | 82 -
src/main/java/htsjdk/samtools/SAMTagUtil.java | 122 -
src/main/java/htsjdk/samtools/SAMTestUtil.java | 128 -
.../java/htsjdk/samtools/SAMTextHeaderCodec.java | 500 -
src/main/java/htsjdk/samtools/SAMTextReader.java | 253 -
src/main/java/htsjdk/samtools/SAMTextWriter.java | 221 -
src/main/java/htsjdk/samtools/SAMTools.java | 119 -
src/main/java/htsjdk/samtools/SAMUtils.java | 1226 -
.../java/htsjdk/samtools/SAMValidationError.java | 291 -
src/main/java/htsjdk/samtools/SQTagUtil.java | 154 -
src/main/java/htsjdk/samtools/SRAFileReader.java | 309 -
src/main/java/htsjdk/samtools/SRAIndex.java | 257 -
src/main/java/htsjdk/samtools/SRAIterator.java | 256 -
.../java/htsjdk/samtools/SamFileHeaderMerger.java | 786 -
.../java/htsjdk/samtools/SamFileValidator.java | 872 -
src/main/java/htsjdk/samtools/SamFiles.java | 98 -
src/main/java/htsjdk/samtools/SamFlagField.java | 203 -
src/main/java/htsjdk/samtools/SamIndexes.java | 94 -
.../java/htsjdk/samtools/SamInputResource.java | 497 -
src/main/java/htsjdk/samtools/SamPairUtil.java | 510 -
src/main/java/htsjdk/samtools/SamReader.java | 621 -
.../java/htsjdk/samtools/SamReaderFactory.java | 568 -
src/main/java/htsjdk/samtools/SamStreams.java | 164 -
.../SecondaryOrSupplementarySkippingIterator.java | 41 -
.../StreamInflatingIndexingOutputStream.java | 103 -
.../samtools/TagValueAndUnsignedArrayFlag.java | 42 -
src/main/java/htsjdk/samtools/TextCigarCodec.java | 91 -
src/main/java/htsjdk/samtools/TextTagCodec.java | 331 -
.../htsjdk/samtools/TextualBAMIndexWriter.java | 185 -
.../java/htsjdk/samtools/ValidationStringency.java | 21 -
.../java/htsjdk/samtools/apps/TimeChannel.java | 58 -
.../htsjdk/samtools/apps/TimeRandomAccessFile.java | 55 -
src/main/java/htsjdk/samtools/cram/CRAIEntry.java | 195 -
src/main/java/htsjdk/samtools/cram/CRAIIndex.java | 267 -
.../java/htsjdk/samtools/cram/CRAMException.java | 22 -
.../cram/build/CompressionHeaderFactory.java | 592 -
.../samtools/cram/build/ContainerFactory.java | 215 -
.../samtools/cram/build/ContainerParser.java | 221 -
.../samtools/cram/build/Cram2SamRecordFactory.java | 227 -
.../samtools/cram/build/CramContainerIterator.java | 77 -
.../java/htsjdk/samtools/cram/build/CramIO.java | 343 -
.../htsjdk/samtools/cram/build/CramNormalizer.java | 347 -
.../cram/build/CramSpanContainerIterator.java | 100 -
.../samtools/cram/build/Sam2CramRecordFactory.java | 374 -
.../java/htsjdk/samtools/cram/build/Utils.java | 54 -
.../samtools/cram/common/CramVersionPolicies.java | 24 -
.../htsjdk/samtools/cram/common/CramVersions.java | 11 -
.../htsjdk/samtools/cram/common/IntHashMap.java | 415 -
.../htsjdk/samtools/cram/common/MutableInt.java | 27 -
.../java/htsjdk/samtools/cram/common/Version.java | 63 -
.../samtools/cram/digest/AbstractSerialDigest.java | 26 -
.../samtools/cram/digest/ByteSumCombine.java | 12 -
.../java/htsjdk/samtools/cram/digest/Combine.java | 6 -
.../samtools/cram/digest/ContentDigests.java | 217 -
.../htsjdk/samtools/cram/digest/Crc32Hasher.java | 42 -
.../samtools/cram/digest/IntegerSumCombine.java | 10 -
.../samtools/cram/digest/MessageDigestHasher.java | 30 -
.../java/htsjdk/samtools/cram/digest/SERIES.java | 34 -
.../samtools/cram/encoding/AbstractBitCodec.java | 56 -
.../samtools/cram/encoding/BetaIntegerCodec.java | 62 -
.../cram/encoding/BetaIntegerEncoding.java | 78 -
.../htsjdk/samtools/cram/encoding/BitCodec.java | 97 -
.../cram/encoding/ByteArrayLenEncoding.java | 146 -
.../cram/encoding/ByteArrayStopEncoding.java | 130 -
.../htsjdk/samtools/cram/encoding/DataSeries.java | 49 -
.../samtools/cram/encoding/DataSeriesMap.java | 29 -
.../samtools/cram/encoding/DataSeriesType.java | 41 -
.../htsjdk/samtools/cram/encoding/Encoding.java | 44 -
.../samtools/cram/encoding/EncodingFactory.java | 118 -
.../cram/encoding/ExternalByteArrayCodec.java | 76 -
.../cram/encoding/ExternalByteArrayEncoding.java | 63 -
.../samtools/cram/encoding/ExternalByteCodec.java | 64 -
.../cram/encoding/ExternalByteEncoding.java | 62 -
.../samtools/cram/encoding/ExternalCompressor.java | 84 -
.../cram/encoding/ExternalIntegerCodec.java | 76 -
.../cram/encoding/ExternalIntegerEncoding.java | 62 -
.../samtools/cram/encoding/ExternalLongCodec.java | 65 -
.../cram/encoding/ExternalLongEncoding.java | 62 -
.../samtools/cram/encoding/GammaIntegerCodec.java | 72 -
.../cram/encoding/GammaIntegerEncoding.java | 73 -
.../samtools/cram/encoding/GolombIntegerCodec.java | 101 -
.../cram/encoding/GolombIntegerEncoding.java | 80 -
.../samtools/cram/encoding/GolombLongCodec.java | 100 -
.../samtools/cram/encoding/GolombLongEncoding.java | 73 -
.../cram/encoding/GolombRiceIntegerCodec.java | 87 -
.../cram/encoding/GolombRiceIntegerEncoding.java | 73 -
.../htsjdk/samtools/cram/encoding/NullCodec.java | 52 -
.../samtools/cram/encoding/NullEncoding.java | 57 -
.../cram/encoding/SubexponentialIntegerCodec.java | 99 -
.../encoding/SubexponentialIntegerEncoding.java | 78 -
.../cram/encoding/huffman/HuffmanCode.java | 99 -
.../cram/encoding/huffman/HuffmanLeaf.java | 28 -
.../cram/encoding/huffman/HuffmanNode.java | 28 -
.../cram/encoding/huffman/HuffmanTree.java | 30 -
.../huffman/codec/CanonicalHuffmanByteCodec.java | 70 -
.../codec/CanonicalHuffmanIntegerCodec.java | 59 -
.../encoding/huffman/codec/HuffmanBitCode.java | 29 -
.../huffman/codec/HuffmanByteEncoding.java | 91 -
.../encoding/huffman/codec/HuffmanByteHelper.java | 178 -
.../encoding/huffman/codec/HuffmanIntHelper.java | 178 -
.../huffman/codec/HuffmanIntegerEncoding.java | 100 -
.../huffman/codec/HuffmanParamsCalculator.java | 137 -
.../samtools/cram/encoding/rans/Constants.java | 7 -
.../htsjdk/samtools/cram/encoding/rans/D04.java | 86 -
.../htsjdk/samtools/cram/encoding/rans/D14.java | 71 -
.../samtools/cram/encoding/rans/Decoding.java | 93 -
.../htsjdk/samtools/cram/encoding/rans/E04.java | 59 -
.../htsjdk/samtools/cram/encoding/rans/E14.java | 88 -
.../samtools/cram/encoding/rans/Encoding.java | 73 -
.../samtools/cram/encoding/rans/Frequencies.java | 331 -
.../htsjdk/samtools/cram/encoding/rans/RANS.java | 172 -
.../htsjdk/samtools/cram/encoding/rans/Utils.java | 34 -
.../cram/encoding/reader/AbstractReader.java | 131 -
.../cram/encoding/reader/CramRecordReader.java | 212 -
.../samtools/cram/encoding/reader/DataReader.java | 44 -
.../cram/encoding/reader/DataReaderFactory.java | 228 -
.../cram/encoding/reader/RefSeqIdReader.java | 242 -
.../encoding/readfeatures/BaseQualityScore.java | 76 -
.../samtools/cram/encoding/readfeatures/Bases.java | 76 -
.../cram/encoding/readfeatures/Deletion.java | 77 -
.../cram/encoding/readfeatures/HardClip.java | 75 -
.../cram/encoding/readfeatures/InsertBase.java | 77 -
.../cram/encoding/readfeatures/Insertion.java | 75 -
.../cram/encoding/readfeatures/Padding.java | 76 -
.../cram/encoding/readfeatures/ReadBase.java | 89 -
.../cram/encoding/readfeatures/ReadFeature.java | 36 -
.../cram/encoding/readfeatures/RefSkip.java | 76 -
.../cram/encoding/readfeatures/Scores.java | 79 -
.../cram/encoding/readfeatures/SoftClip.java | 77 -
.../cram/encoding/readfeatures/Substitution.java | 110 -
.../samtools/cram/encoding/writer/DataWriter.java | 41 -
.../cram/encoding/writer/DataWriterFactory.java | 109 -
.../samtools/cram/encoding/writer/Writer.java | 270 -
.../htsjdk/samtools/cram/io/BitInputStream.java | 51 -
.../htsjdk/samtools/cram/io/BitOutputStream.java | 73 -
.../htsjdk/samtools/cram/io/CRC32InputStream.java | 77 -
.../htsjdk/samtools/cram/io/CRC32OutputStream.java | 55 -
.../samtools/cram/io/CountingInputStream.java | 83 -
.../java/htsjdk/samtools/cram/io/CramArray.java | 41 -
src/main/java/htsjdk/samtools/cram/io/CramInt.java | 78 -
.../samtools/cram/io/DefaultBitInputStream.java | 115 -
.../samtools/cram/io/DefaultBitOutputStream.java | 178 -
.../cram/io/ExposedByteArrayOutputStream.java | 26 -
.../samtools/cram/io/ExternalCompression.java | 152 -
src/main/java/htsjdk/samtools/cram/io/ITF8.java | 186 -
.../htsjdk/samtools/cram/io/InputStreamUtils.java | 80 -
src/main/java/htsjdk/samtools/cram/io/LTF8.java | 193 -
.../htsjdk/samtools/cram/lossy/BaseCategory.java | 57 -
.../samtools/cram/lossy/BaseCategoryType.java | 30 -
.../java/htsjdk/samtools/cram/lossy/Binning.java | 76 -
.../samtools/cram/lossy/PreservationPolicy.java | 42 -
.../cram/lossy/QualityScorePreservation.java | 410 -
.../samtools/cram/lossy/QualityScoreTreatment.java | 47 -
.../cram/lossy/QualityScoreTreatmentType.java | 22 -
.../htsjdk/samtools/cram/lossy/ReadCategory.java | 50 -
.../samtools/cram/lossy/ReadCategoryType.java | 29 -
.../samtools/cram/ref/CRAMReferenceSource.java | 22 -
.../htsjdk/samtools/cram/ref/EnaRefService.java | 122 -
.../cram/ref/InMemoryReferenceSequenceFile.java | 102 -
.../htsjdk/samtools/cram/ref/ReferenceRegion.java | 93 -
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 280 -
.../htsjdk/samtools/cram/ref/ReferenceTracks.java | 172 -
.../samtools/cram/structure/AlignmentSpan.java | 92 -
.../java/htsjdk/samtools/cram/structure/Block.java | 323 -
.../cram/structure/BlockCompressionMethod.java | 22 -
.../samtools/cram/structure/BlockContentType.java | 22 -
.../samtools/cram/structure/CompressionHeader.java | 299 -
.../htsjdk/samtools/cram/structure/Container.java | 81 -
.../samtools/cram/structure/ContainerHeaderIO.java | 96 -
.../samtools/cram/structure/ContainerIO.java | 237 -
.../cram/structure/CramCompressionRecord.java | 348 -
.../htsjdk/samtools/cram/structure/CramHeader.java | 123 -
.../htsjdk/samtools/cram/structure/EncodingID.java | 64 -
.../samtools/cram/structure/EncodingKey.java | 40 -
.../samtools/cram/structure/EncodingParams.java | 39 -
.../htsjdk/samtools/cram/structure/ReadTag.java | 487 -
.../java/htsjdk/samtools/cram/structure/Slice.java | 245 -
.../htsjdk/samtools/cram/structure/SliceIO.java | 153 -
.../cram/structure/SubstitutionMatrix.java | 179 -
.../htsjdk/samtools/example/ExampleSamUsage.java | 118 -
.../htsjdk/samtools/example/PrintReadsExample.java | 98 -
.../htsjdk/samtools/fastq/AsyncFastqWriter.java | 20 -
.../htsjdk/samtools/fastq/BasicFastqWriter.java | 89 -
.../java/htsjdk/samtools/fastq/FastqConstants.java | 49 -
.../java/htsjdk/samtools/fastq/FastqReader.java | 199 -
.../java/htsjdk/samtools/fastq/FastqRecord.java | 124 -
.../java/htsjdk/samtools/fastq/FastqWriter.java | 13 -
.../htsjdk/samtools/fastq/FastqWriterFactory.java | 31 -
.../samtools/filter/AbstractJavascriptFilter.java | 159 -
.../htsjdk/samtools/filter/AggregateFilter.java | 79 -
.../java/htsjdk/samtools/filter/AlignedFilter.java | 87 -
.../samtools/filter/DuplicateReadFilter.java | 52 -
.../filter/FailsVendorReadQualityFilter.java | 57 -
.../htsjdk/samtools/filter/FilteringIterator.java | 53 -
.../samtools/filter/FilteringSamIterator.java | 155 -
.../htsjdk/samtools/filter/InsertSizeFilter.java | 31 -
.../htsjdk/samtools/filter/IntervalFilter.java | 102 -
.../samtools/filter/IntervalKeepPairFilter.java | 108 -
.../samtools/filter/JavascriptSamRecordFilter.java | 101 -
.../samtools/filter/MappingQualityFilter.java | 25 -
.../samtools/filter/NotPrimaryAlignmentFilter.java | 54 -
.../samtools/filter/OverclippedReadFilter.java | 76 -
.../htsjdk/samtools/filter/ReadNameFilter.java | 120 -
.../htsjdk/samtools/filter/SamRecordFilter.java | 53 -
.../samtools/filter/SecondaryAlignmentFilter.java | 20 -
.../filter/SecondaryOrSupplementaryFilter.java | 32 -
.../htsjdk/samtools/filter/SolexaNoiseFilter.java | 66 -
.../java/htsjdk/samtools/filter/TagFilter.java | 85 -
.../samtools/filter/WholeReadClippedFilter.java | 64 -
src/main/java/htsjdk/samtools/liftover/Chain.java | 414 -
.../java/htsjdk/samtools/liftover/LiftOver.java | 319 -
src/main/java/htsjdk/samtools/metrics/Header.java | 43 -
.../java/htsjdk/samtools/metrics/MetricBase.java | 125 -
.../java/htsjdk/samtools/metrics/MetricsFile.java | 594 -
.../java/htsjdk/samtools/metrics/StringHeader.java | 72 -
.../htsjdk/samtools/metrics/VersionHeader.java | 81 -
.../reference/AbstractFastaSequenceFile.java | 158 -
.../samtools/reference/FastaSequenceFile.java | 172 -
.../samtools/reference/FastaSequenceIndex.java | 323 -
.../reference/IndexedFastaSequenceFile.java | 328 -
.../samtools/reference/ReferenceSequence.java | 84 -
.../samtools/reference/ReferenceSequenceFile.java | 90 -
.../reference/ReferenceSequenceFileFactory.java | 136 -
.../reference/ReferenceSequenceFileWalker.java | 111 -
.../seekablestream/ByteArraySeekableStream.java | 99 -
.../seekablestream/ISeekableStreamFactory.java | 33 -
.../seekablestream/SeekableBufferedStream.java | 132 -
.../samtools/seekablestream/SeekableFTPStream.java | 120 -
.../seekablestream/SeekableFTPStreamHelper.java | 166 -
.../seekablestream/SeekableFileStream.java | 128 -
.../seekablestream/SeekableHTTPStream.java | 186 -
.../seekablestream/SeekableMemoryStream.java | 64 -
.../seekablestream/SeekablePathStream.java | 121 -
.../samtools/seekablestream/SeekableStream.java | 69 -
.../seekablestream/SeekableStreamFactory.java | 97 -
.../samtools/seekablestream/UserPasswordInput.java | 31 -
.../java/htsjdk/samtools/sra/ReferenceCache.java | 46 -
.../java/htsjdk/samtools/sra/SRAAccession.java | 177 -
.../htsjdk/samtools/sra/SRAAlignmentIterator.java | 209 -
.../samtools/sra/SRAIndexedSequenceFile.java | 112 -
.../java/htsjdk/samtools/sra/SRALazyRecord.java | 1056 -
.../samtools/sra/SRAUnalignmentIterator.java | 181 -
src/main/java/htsjdk/samtools/sra/SRAUtils.java | 83 -
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 137 -
.../htsjdk/samtools/util/AbstractIterator.java | 85 -
.../htsjdk/samtools/util/AbstractLocusInfo.java | 146 -
.../samtools/util/AbstractLocusIterator.java | 572 -
.../samtools/util/AbstractProgressLogger.java | 119 -
.../samtools/util/AbstractRecordAndOffset.java | 130 -
.../java/htsjdk/samtools/util/AsciiWriter.java | 83 -
.../samtools/util/AsyncBufferedIterator.java | 281 -
.../java/htsjdk/samtools/util/BinaryCodec.java | 670 -
.../util/BlockCompressedFilePointerUtil.java | 101 -
.../samtools/util/BlockCompressedInputStream.java | 513 -
.../samtools/util/BlockCompressedOutputStream.java | 392 -
.../util/BlockCompressedStreamConstants.java | 118 -
.../java/htsjdk/samtools/util/BlockGunzipper.java | 132 -
.../htsjdk/samtools/util/BufferedLineReader.java | 115 -
src/main/java/htsjdk/samtools/util/CigarUtil.java | 294 -
.../htsjdk/samtools/util/CloseableIterator.java | 63 -
src/main/java/htsjdk/samtools/util/CloserUtil.java | 81 -
src/main/java/htsjdk/samtools/util/CodeUtil.java | 14 -
.../java/htsjdk/samtools/util/CollectionUtil.java | 191 -
.../java/htsjdk/samtools/util/ComparableTuple.java | 28 -
src/main/java/htsjdk/samtools/util/CoordMath.java | 76 -
.../htsjdk/samtools/util/CoordSpanInputSteam.java | 100 -
.../samtools/util/CustomGzipOutputStream.java | 24 -
src/main/java/htsjdk/samtools/util/DateParser.java | 337 -
.../htsjdk/samtools/util/DelegatingIterator.java | 35 -
.../java/htsjdk/samtools/util/DiskBackedQueue.java | 406 -
.../htsjdk/samtools/util/EdgeReadIterator.java | 228 -
.../samtools/util/EdgingRecordAndOffset.java | 219 -
.../java/htsjdk/samtools/util/FastLineReader.java | 171 -
.../htsjdk/samtools/util/FastqQualityFormat.java | 36 -
.../samtools/util/FileAppendStreamLRUCache.java | 78 -
src/main/java/htsjdk/samtools/util/FormatUtil.java | 203 -
src/main/java/htsjdk/samtools/util/Histogram.java | 567 -
src/main/java/htsjdk/samtools/util/HttpUtils.java | 80 -
src/main/java/htsjdk/samtools/util/IOUtil.java | 946 -
src/main/java/htsjdk/samtools/util/Interval.java | 202 -
.../java/htsjdk/samtools/util/IntervalList.java | 790 -
.../util/IntervalListReferenceSequenceMask.java | 125 -
.../java/htsjdk/samtools/util/IntervalTree.java | 1227 -
.../java/htsjdk/samtools/util/IntervalTreeMap.java | 331 -
.../java/htsjdk/samtools/util/IntervalUtil.java | 76 -
.../java/htsjdk/samtools/util/Iso8601Date.java | 65 -
.../java/htsjdk/samtools/util/IterableAdapter.java | 29 -
.../htsjdk/samtools/util/IterableOnceIterator.java | 42 -
src/main/java/htsjdk/samtools/util/Iterables.java | 24 -
src/main/java/htsjdk/samtools/util/Lazy.java | 40 -
src/main/java/htsjdk/samtools/util/LineReader.java | 51 -
src/main/java/htsjdk/samtools/util/ListMap.java | 48 -
src/main/java/htsjdk/samtools/util/Locatable.java | 25 -
.../java/htsjdk/samtools/util/LocationAware.java | 26 -
src/main/java/htsjdk/samtools/util/Locus.java | 36 -
.../java/htsjdk/samtools/util/LocusComparator.java | 41 -
src/main/java/htsjdk/samtools/util/LocusImpl.java | 49 -
src/main/java/htsjdk/samtools/util/Log.java | 214 -
.../samtools/util/Md5CalculatingInputStream.java | 133 -
.../samtools/util/Md5CalculatingOutputStream.java | 119 -
.../java/htsjdk/samtools/util/MergingIterator.java | 145 -
src/main/java/htsjdk/samtools/util/Murmur3.java | 119 -
.../java/htsjdk/samtools/util/OverlapDetector.java | 193 -
.../java/htsjdk/samtools/util/PeekIterator.java | 85 -
.../htsjdk/samtools/util/PeekableIterator.java | 79 -
.../samtools/util/PositionalOutputStream.java | 65 -
.../java/htsjdk/samtools/util/ProcessExecutor.java | 243 -
.../java/htsjdk/samtools/util/ProgressLogger.java | 52 -
.../samtools/util/ProgressLoggerInterface.java | 38 -
.../samtools/util/QualityEncodingDetector.java | 405 -
.../java/htsjdk/samtools/util/QualityUtil.java | 77 -
.../samtools/util/ReferenceSequenceMask.java | 55 -
.../htsjdk/samtools/util/RelativeIso8601Date.java | 203 -
.../htsjdk/samtools/util/ResourceLimitedMap.java | 105 -
.../samtools/util/ResourceLimitedMapFunctor.java | 47 -
.../htsjdk/samtools/util/RuntimeEOFException.java | 46 -
.../htsjdk/samtools/util/RuntimeIOException.java | 46 -
.../samtools/util/RuntimeScriptException.java | 45 -
.../htsjdk/samtools/util/SamLocusIterator.java | 292 -
.../util/SamRecordIntervalIteratorFactory.java | 157 -
.../samtools/util/SamRecordTrackingBuffer.java | 321 -
.../htsjdk/samtools/util/SamRecordWithOrdinal.java | 56 -
.../java/htsjdk/samtools/util/SequenceUtil.java | 1031 -
.../java/htsjdk/samtools/util/SnappyLoader.java | 127 -
.../samtools/util/SolexaQualityConverter.java | 129 -
.../htsjdk/samtools/util/SortingCollection.java | 514 -
.../samtools/util/SortingLongCollection.java | 349 -
src/main/java/htsjdk/samtools/util/StopWatch.java | 76 -
.../htsjdk/samtools/util/StringLineReader.java | 99 -
src/main/java/htsjdk/samtools/util/StringUtil.java | 603 -
.../htsjdk/samtools/util/TempStreamFactory.java | 83 -
src/main/java/htsjdk/samtools/util/TestUtil.java | 98 -
.../java/htsjdk/samtools/util/TrimmingUtil.java | 67 -
src/main/java/htsjdk/samtools/util/Tuple.java | 41 -
.../util/WholeGenomeReferenceSequenceMask.java | 80 -
.../java/htsjdk/samtools/util/ftp/FTPClient.java | 240 -
.../java/htsjdk/samtools/util/ftp/FTPReply.java | 113 -
.../java/htsjdk/samtools/util/ftp/FTPStream.java | 53 -
.../java/htsjdk/samtools/util/ftp/FTPUtils.java | 154 -
.../htsjdk/samtools/util/zip/DeflaterFactory.java | 48 -
.../java/htsjdk/tribble/AbstractFeatureCodec.java | 50 -
.../java/htsjdk/tribble/AbstractFeatureReader.java | 193 -
.../java/htsjdk/tribble/AsciiFeatureCodec.java | 92 -
.../java/htsjdk/tribble/BinaryFeatureCodec.java | 52 -
.../htsjdk/tribble/CloseableTribbleIterator.java | 27 -
src/main/java/htsjdk/tribble/Feature.java | 43 -
src/main/java/htsjdk/tribble/FeatureCodec.java | 136 -
.../java/htsjdk/tribble/FeatureCodecHeader.java | 83 -
src/main/java/htsjdk/tribble/FeatureReader.java | 41 -
src/main/java/htsjdk/tribble/NameAwareCodec.java | 37 -
src/main/java/htsjdk/tribble/SimpleFeature.java | 53 -
.../java/htsjdk/tribble/TabixFeatureReader.java | 217 -
src/main/java/htsjdk/tribble/Tribble.java | 100 -
src/main/java/htsjdk/tribble/TribbleException.java | 139 -
.../tribble/TribbleIndexedFeatureReader.java | 573 -
.../java/htsjdk/tribble/annotation/Strand.java | 52 -
src/main/java/htsjdk/tribble/bed/BEDCodec.java | 242 -
src/main/java/htsjdk/tribble/bed/BEDFeature.java | 55 -
.../java/htsjdk/tribble/bed/FullBEDFeature.java | 433 -
.../java/htsjdk/tribble/bed/SimpleBEDFeature.java | 140 -
.../java/htsjdk/tribble/example/CountRecords.java | 200 -
.../htsjdk/tribble/example/ExampleBinaryCodec.java | 128 -
.../java/htsjdk/tribble/example/IndexToTable.java | 72 -
.../htsjdk/tribble/example/IndicesAreEqual.java | 76 -
.../tribble/example/ProfileIndexReading.java | 66 -
.../exception/CodecLineParsingException.java | 50 -
.../tribble/exception/UnsortedFileException.java | 45 -
.../htsjdk/tribble/gelitext/DiploidGenotype.java | 66 -
.../htsjdk/tribble/gelitext/GeliTextCodec.java | 117 -
.../htsjdk/tribble/gelitext/GeliTextFeature.java | 148 -
.../java/htsjdk/tribble/index/AbstractIndex.java | 451 -
src/main/java/htsjdk/tribble/index/Block.java | 82 -
src/main/java/htsjdk/tribble/index/ChrIndex.java | 55 -
.../htsjdk/tribble/index/DynamicIndexCreator.java | 209 -
src/main/java/htsjdk/tribble/index/Index.java | 99 -
.../java/htsjdk/tribble/index/IndexCreator.java | 57 -
.../java/htsjdk/tribble/index/IndexFactory.java | 515 -
.../java/htsjdk/tribble/index/MutableIndex.java | 36 -
.../htsjdk/tribble/index/TribbleIndexCreator.java | 53 -
.../htsjdk/tribble/index/interval/Interval.java | 115 -
.../index/interval/IntervalIndexCreator.java | 159 -
.../tribble/index/interval/IntervalTree.java | 551 -
.../tribble/index/interval/IntervalTreeIndex.java | 214 -
.../htsjdk/tribble/index/linear/LinearIndex.java | 434 -
.../tribble/index/linear/LinearIndexCreator.java | 126 -
.../htsjdk/tribble/index/tabix/TabixFormat.java | 109 -
.../htsjdk/tribble/index/tabix/TabixIndex.java | 366 -
.../tribble/index/tabix/TabixIndexCreator.java | 202 -
.../htsjdk/tribble/readers/AsciiLineReader.java | 185 -
.../tribble/readers/AsciiLineReaderIterator.java | 101 -
.../java/htsjdk/tribble/readers/LineIterator.java | 12 -
.../htsjdk/tribble/readers/LineIteratorImpl.java | 34 -
.../java/htsjdk/tribble/readers/LineReader.java | 43 -
.../htsjdk/tribble/readers/LineReaderUtil.java | 56 -
.../tribble/readers/LongLineBufferedReader.java | 490 -
.../java/htsjdk/tribble/readers/Positional.java | 60 -
.../tribble/readers/PositionalBufferedStream.java | 229 -
.../tribble/readers/SynchronousLineReader.java | 61 -
.../tribble/readers/TabixIteratorLineReader.java | 54 -
.../java/htsjdk/tribble/readers/TabixReader.java | 526 -
src/main/java/htsjdk/tribble/readme.txt | 1 -
src/main/java/htsjdk/tribble/util/FTPHelper.java | 55 -
src/main/java/htsjdk/tribble/util/HTTPHelper.java | 152 -
.../tribble/util/LittleEndianInputStream.java | 144 -
.../tribble/util/LittleEndianOutputStream.java | 120 -
src/main/java/htsjdk/tribble/util/MathUtils.java | 66 -
.../java/htsjdk/tribble/util/ParsingUtils.java | 478 -
.../java/htsjdk/tribble/util/RemoteURLHelper.java | 55 -
src/main/java/htsjdk/tribble/util/TabixUtils.java | 115 -
src/main/java/htsjdk/tribble/util/URLHelper.java | 56 -
.../util/popgen/HardyWeinbergCalculation.java | 149 -
src/main/java/htsjdk/variant/bcf2/BCF2Codec.java | 491 -
src/main/java/htsjdk/variant/bcf2/BCF2Decoder.java | 362 -
.../variant/bcf2/BCF2GenotypeFieldDecoders.java | 278 -
.../variant/bcf2/BCF2LazyGenotypesDecoder.java | 99 -
src/main/java/htsjdk/variant/bcf2/BCF2Type.java | 214 -
src/main/java/htsjdk/variant/bcf2/BCF2Utils.java | 336 -
src/main/java/htsjdk/variant/bcf2/BCFVersion.java | 105 -
.../variant/example/PrintVariantsExample.java | 103 -
.../java/htsjdk/variant/utils/GeneralUtils.java | 246 -
.../utils/SAMSequenceDictionaryExtractor.java | 137 -
.../java/htsjdk/variant/variantcontext/Allele.java | 546 -
.../htsjdk/variant/variantcontext/CommonInfo.java | 341 -
.../variant/variantcontext/FastGenotype.java | 173 -
.../htsjdk/variant/variantcontext/Genotype.java | 670 -
.../variant/variantcontext/GenotypeBuilder.java | 421 -
.../variantcontext/GenotypeJEXLContext.java | 59 -
.../variantcontext/GenotypeLikelihoods.java | 578 -
.../variant/variantcontext/GenotypeType.java | 47 -
.../variant/variantcontext/GenotypesContext.java | 719 -
.../htsjdk/variant/variantcontext/JEXLMap.java | 228 -
.../variantcontext/JexlMissingValueTreatment.java | 39 -
.../variantcontext/LazyGenotypesContext.java | 226 -
.../variantcontext/StructuralVariantType.java | 47 -
.../variant/variantcontext/VariantContext.java | 1734 --
.../variantcontext/VariantContextBuilder.java | 498 -
.../variantcontext/VariantContextComparator.java | 105 -
.../variantcontext/VariantContextUtils.java | 483 -
.../variant/variantcontext/VariantJEXLContext.java | 102 -
.../variantcontext/filter/CompoundFilter.java | 74 -
.../variantcontext/filter/FilteringIterator.java | 47 -
.../filter/FilteringVariantContextIterator.java | 127 -
.../filter/GenotypeQualityFilter.java | 79 -
.../filter/HeterozygosityFilter.java | 84 -
.../filter/JavascriptVariantFilter.java | 97 -
.../filter/PassingVariantFilter.java | 44 -
.../variant/variantcontext/filter/SnpFilter.java | 44 -
.../filter/VariantContextFilter.java | 43 -
.../writer/AsyncVariantContextWriter.java | 54 -
.../variant/variantcontext/writer/BCF2Encoder.java | 261 -
.../variantcontext/writer/BCF2FieldEncoder.java | 455 -
.../variantcontext/writer/BCF2FieldWriter.java | 323 -
.../writer/BCF2FieldWriterManager.java | 180 -
.../variant/variantcontext/writer/BCF2Writer.java | 443 -
.../writer/IndexingVariantContextWriter.java | 180 -
.../writer/IntGenotypeFieldAccessors.java | 97 -
.../variant/variantcontext/writer/Options.java | 41 -
.../writer/SortingVariantContextWriter.java | 66 -
.../writer/SortingVariantContextWriterBase.java | 201 -
.../variant/variantcontext/writer/VCFWriter.java | 231 -
.../writer/VariantContextWriter.java | 51 -
.../writer/VariantContextWriterBuilder.java | 537 -
.../writer/VariantContextWriterFactory.java | 282 -
.../java/htsjdk/variant/vcf/AbstractVCFCodec.java | 791 -
src/main/java/htsjdk/variant/vcf/VCF3Codec.java | 134 -
src/main/java/htsjdk/variant/vcf/VCFCodec.java | 161 -
.../htsjdk/variant/vcf/VCFCompoundHeaderLine.java | 301 -
src/main/java/htsjdk/variant/vcf/VCFConstants.java | 130 -
.../htsjdk/variant/vcf/VCFContigHeaderLine.java | 118 -
src/main/java/htsjdk/variant/vcf/VCFEncoder.java | 382 -
.../java/htsjdk/variant/vcf/VCFFileReader.java | 153 -
.../htsjdk/variant/vcf/VCFFilterHeaderLine.java | 79 -
.../htsjdk/variant/vcf/VCFFormatHeaderLine.java | 63 -
src/main/java/htsjdk/variant/vcf/VCFHeader.java | 574 -
.../java/htsjdk/variant/vcf/VCFHeaderLine.java | 174 -
.../htsjdk/variant/vcf/VCFHeaderLineCount.java | 33 -
.../variant/vcf/VCFHeaderLineTranslator.java | 183 -
.../java/htsjdk/variant/vcf/VCFHeaderLineType.java | 33 -
.../java/htsjdk/variant/vcf/VCFHeaderVersion.java | 138 -
.../java/htsjdk/variant/vcf/VCFIDHeaderLine.java | 31 -
.../java/htsjdk/variant/vcf/VCFInfoHeaderLine.java | 61 -
.../java/htsjdk/variant/vcf/VCFRecordCodec.java | 64 -
.../htsjdk/variant/vcf/VCFSimpleHeaderLine.java | 127 -
.../htsjdk/variant/vcf/VCFStandardHeaderLines.java | 233 -
src/main/java/htsjdk/variant/vcf/VCFUtils.java | 209 -
.../htsjdk/cram/io/ExternalCompressionTest.java | 30 -
.../htsjdk/samtools/AbstractBAMFileIndexTest.java | 62 -
.../java/htsjdk/samtools/BAMCigarOverflowTest.java | 29 -
.../java/htsjdk/samtools/BAMFileIndexTest.java | 527 -
.../java/htsjdk/samtools/BAMFileWriterTest.java | 192 -
.../java/htsjdk/samtools/BAMIndexWriterTest.java | 227 -
src/test/java/htsjdk/samtools/BAMIteratorTest.java | 71 -
...AMQueryMultipleIntervalsIteratorFilterTest.java | 146 -
.../java/htsjdk/samtools/BAMRemoteFileTest.java | 327 -
src/test/java/htsjdk/samtools/BinTest.java | 39 -
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 87 -
.../java/htsjdk/samtools/CRAMCRAIIndexerTest.java | 183 -
.../java/htsjdk/samtools/CRAMComplianceTest.java | 150 -
.../samtools/CRAMContainerStreamWriterTest.java | 184 -
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 158 -
.../java/htsjdk/samtools/CRAMFileBAIIndexTest.java | 301 -
.../htsjdk/samtools/CRAMFileCRAIIndexTest.java | 368 -
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 231 -
.../java/htsjdk/samtools/CRAMFileWriterTest.java | 282 -
.../samtools/CRAMFileWriterWithIndexTest.java | 209 -
.../java/htsjdk/samtools/CRAMIndexQueryTest.java | 708 -
src/test/java/htsjdk/samtools/ChunkTest.java | 78 -
src/test/java/htsjdk/samtools/CigarCodecTest.java | 110 -
src/test/java/htsjdk/samtools/CigarTest.java | 118 -
.../htsjdk/samtools/DownsamplingIteratorTests.java | 87 -
.../htsjdk/samtools/DuplicateSetIteratorTest.java | 63 -
.../java/htsjdk/samtools/GenomicIndexUtilTest.java | 50 -
...MergingSamRecordIteratorGroupCollisionTest.java | 528 -
.../samtools/MergingSamRecordIteratorTest.java | 312 -
.../htsjdk/samtools/ProgramRecordChainingTest.java | 57 -
.../samtools/SAMBinaryTagAndValueUnitTest.java | 183 -
src/test/java/htsjdk/samtools/SAMCloneTest.java | 52 -
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 307 -
src/test/java/htsjdk/samtools/SAMFlagTest.java | 42 -
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 375 -
.../samtools/SAMRecordDuplicateComparatorTest.java | 233 -
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 1041 -
.../samtools/SAMSequenceDictionaryCodecTest.java | 122 -
.../htsjdk/samtools/SAMSequenceDictionaryTest.java | 147 -
.../java/htsjdk/samtools/SAMTextReaderTest.java | 137 -
.../java/htsjdk/samtools/SAMTextWriterTest.java | 130 -
src/test/java/htsjdk/samtools/SAMUtilsTest.java | 250 -
.../htsjdk/samtools/SamFileHeaderMergerTest.java | 265 -
src/test/java/htsjdk/samtools/SamFilesTest.java | 91 -
.../java/htsjdk/samtools/SamFlagFieldTest.java | 150 -
.../samtools/SamHeaderRecordComparatorTest.java | 72 -
src/test/java/htsjdk/samtools/SamIndexesTest.java | 193 -
src/test/java/htsjdk/samtools/SamPairUtilTest.java | 251 -
.../java/htsjdk/samtools/SamReaderFactoryTest.java | 468 -
.../java/htsjdk/samtools/SamReaderSortTest.java | 102 -
src/test/java/htsjdk/samtools/SamReaderTest.java | 170 -
src/test/java/htsjdk/samtools/SamSpecIntTest.java | 97 -
src/test/java/htsjdk/samtools/SamStreamsTest.java | 124 -
.../SequenceNameTruncationAndValidationTest.java | 98 -
.../java/htsjdk/samtools/ValidateSamFileTest.java | 547 -
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 144 -
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 220 -
.../samtools/cram/LosslessRoundTripTest.java | 68 -
.../java/htsjdk/samtools/cram/VersionTest.java | 106 -
.../cram/build/CompressionHeaderFactoryTest.java | 208 -
.../samtools/cram/build/ContainerFactoryTest.java | 134 -
.../samtools/cram/build/ContainerParserTest.java | 185 -
.../htsjdk/samtools/cram/build/CramIOTest.java | 82 -
.../cram/encoding/huffman/codec/HuffmanTest.java | 106 -
.../samtools/cram/encoding/rans/RansTest.java | 228 -
.../java/htsjdk/samtools/cram/io/ITF8Test.java | 101 -
.../java/htsjdk/samtools/cram/io/LTF8Test.java | 80 -
.../cram/lossy/QualityScorePreservationTest.java | 162 -
.../samtools/cram/ref/EnaRefServiceTest.java | 15 -
.../cram/structure/CramCompressionRecordTest.java | 68 -
.../samtools/cram/structure/ReadTagTest.java | 138 -
.../htsjdk/samtools/cram/structure/SliceTests.java | 70 -
.../cram/structure/SubstitutionMatrixTest.java | 105 -
.../htsjdk/samtools/fastq/FastqRecordTest.java | 204 -
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 -
.../filter/FailsVendorReadQualityFilterTest.java | 65 -
.../samtools/filter/InsertSizeFilterTest.java | 43 -
.../filter/IntervalKeepPairFilterTest.java | 123 -
.../filter/JavascriptSamRecordFilterTest.java | 74 -
.../samtools/filter/MappingQualityFilterTest.java | 39 -
.../samtools/filter/OverclippedReadFilterTest.java | 83 -
.../samtools/filter/SolexaNoiseFilterTest.java | 73 -
.../java/htsjdk/samtools/filter/TagFilterTest.java | 77 -
.../htsjdk/samtools/liftover/LiftOverTest.java | 468 -
.../htsjdk/samtools/metrics/MetricBaseTest.java | 75 -
.../htsjdk/samtools/metrics/MetricsFileTest.java | 213 -
.../htsjdk/samtools/metrics/StringHeaderTest.java | 19 -
.../htsjdk/samtools/metrics/VersionHeaderTest.java | 22 -
.../reference/FakeReferenceSequenceFile.java | 77 -
.../samtools/reference/FastaSequenceFileTest.java | 85 -
.../samtools/reference/FastaSequenceIndexTest.java | 256 -
.../reference/InMemoryReferenceSequenceFile.java | 66 -
.../reference/IndexedFastaSequenceFileTest.java | 308 -
.../ReferenceSequenceFileFactoryTests.java | 39 -
.../reference/ReferenceSequenceFileWalkerTest.java | 73 -
.../samtools/reference/ReferenceSequenceTests.java | 98 -
.../seekablestream/SeekableBufferedStreamTest.java | 162 -
.../seekablestream/SeekableFTPStreamTest.java | 106 -
.../seekablestream/SeekableFileStreamTest.java | 52 -
.../seekablestream/SeekableMemoryStreamTest.java | 93 -
.../seekablestream/SeekablePathStreamTest.java | 51 -
.../seekablestream/SeekableStreamFactoryTest.java | 45 -
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 89 -
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 28 -
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 134 -
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 51 -
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 73 -
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 95 -
src/test/java/htsjdk/samtools/sra/SRATest.java | 434 -
.../samtools/util/AbstractLocusInfoTest.java | 79 -
.../util/AbstractLocusIteratorTestTemplate.java | 68 -
.../samtools/util/AbstractRecordAndOffsetTest.java | 63 -
.../samtools/util/AsyncBufferedIteratorTest.java | 115 -
.../java/htsjdk/samtools/util/AsyncWriterTest.java | 77 -
.../java/htsjdk/samtools/util/BinaryCodecTest.java | 287 -
.../util/BlockCompressedFilePointerUtilTest.java | 96 -
.../util/BlockCompressedOutputStreamTest.java | 214 -
.../util/BlockCompressedTerminatorTest.java | 59 -
.../java/htsjdk/samtools/util/CigarUtilTest.java | 143 -
.../samtools/util/CloseableIteratorTest.java | 31 -
.../java/htsjdk/samtools/util/CodeUtilTest.java | 15 -
.../htsjdk/samtools/util/ComparableTupleTest.java | 61 -
.../samtools/util/CoordSpanInputSteamTest.java | 108 -
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 132 -
.../htsjdk/samtools/util/EdgeReadIteratorTest.java | 402 -
.../samtools/util/EdgingRecordAndOffsetTest.java | 94 -
.../java/htsjdk/samtools/util/HistogramTest.java | 366 -
.../htsjdk/samtools/util/IntervalListTest.java | 520 -
.../htsjdk/samtools/util/IntervalTreeMapTest.java | 55 -
.../htsjdk/samtools/util/IntervalTreeTest.java | 187 -
src/test/java/htsjdk/samtools/util/IoUtilTest.java | 190 -
.../java/htsjdk/samtools/util/Iso8601DateTest.java | 57 -
src/test/java/htsjdk/samtools/util/IupacTest.java | 77 -
.../htsjdk/samtools/util/MergingIteratorTest.java | 175 -
.../htsjdk/samtools/util/OverlapDetectorTest.java | 240 -
.../samtools/util/PositionalOutputStreamTest.java | 62 -
.../samtools/util/QualityEncodingDetectorTest.java | 109 -
.../samtools/util/RelativeIso8601DateTest.java | 53 -
.../htsjdk/samtools/util/SamLocusIteratorTest.java | 673 -
.../htsjdk/samtools/util/SequenceUtilTest.java | 453 -
.../samtools/util/SolexaQualityConverterTest.java | 86 -
.../samtools/util/SortingCollectionTest.java | 230 -
.../samtools/util/SortingLongCollectionTest.java | 119 -
.../htsjdk/samtools/util/StringLineReaderTest.java | 119 -
.../java/htsjdk/samtools/util/StringUtilTest.java | 122 -
.../htsjdk/samtools/util/TrimmingUtilTest.java | 70 -
src/test/java/htsjdk/samtools/util/TupleTest.java | 62 -
.../htsjdk/tribble/AbstractFeatureReaderTest.java | 112 -
.../java/htsjdk/tribble/BinaryFeaturesTest.java | 62 -
.../java/htsjdk/tribble/FeatureReaderTest.java | 168 -
src/test/java/htsjdk/tribble/TestUtils.java | 28 -
.../tribble/TribbleIndexFeatureReaderTest.java | 88 -
src/test/java/htsjdk/tribble/TribbleTest.java | 31 -
src/test/java/htsjdk/tribble/bed/BEDCodecTest.java | 240 -
.../java/htsjdk/tribble/gelitext/GeliTextTest.java | 100 -
.../htsjdk/tribble/index/IndexFactoryTest.java | 120 -
src/test/java/htsjdk/tribble/index/IndexTest.java | 97 -
.../tribble/index/interval/IntervalTreeTest.java | 153 -
.../tribble/index/linear/LinearIndexTest.java | 243 -
.../htsjdk/tribble/index/tabix/TabixIndexTest.java | 144 -
.../tribble/readers/AsciiLineReaderTest.java | 52 -
.../readers/LongLineBufferedReaderTest.java | 32 -
.../readers/PositionalBufferedStreamTest.java | 121 -
.../java/htsjdk/tribble/readers/ReaderTest.java | 183 -
.../readers/SynchronousLineReaderUnitTest.java | 39 -
.../htsjdk/tribble/readers/TabixReaderTest.java | 162 -
.../java/htsjdk/tribble/util/ParsingUtilsTest.java | 163 -
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 247 -
.../java/htsjdk/tribble/util/ftp/FTPUtilsTest.java | 31 -
.../util/popgen/HardyWeinbergCalculationTest.java | 41 -
.../htsjdk/variant/PrintVariantsExampleTest.java | 65 -
src/test/java/htsjdk/variant/VariantBaseTest.java | 278 -
.../variant/bcf2/BCF2EncoderDecoderUnitTest.java | 587 -
.../htsjdk/variant/bcf2/BCF2UtilsUnitTest.java | 228 -
.../utils/SAMSequenceDictionaryExtractorTest.java | 65 -
.../variant/variantcontext/AlleleUnitTest.java | 262 -
.../variantcontext/GenotypeBuilderTest.java | 75 -
.../GenotypeLikelihoodsUnitTest.java | 337 -
.../variant/variantcontext/GenotypeUnitTest.java | 107 -
.../variantcontext/GenotypesContextUnitTest.java | 318 -
.../variantcontext/VariantContextBuilderTest.java | 65 -
.../variantcontext/VariantContextTestProvider.java | 1014 -
.../variantcontext/VariantContextUnitTest.java | 1621 -
.../variantcontext/VariantJEXLContextUnitTest.java | 312 -
.../variantcontext/filter/AllFailFilter.java | 41 -
.../variantcontext/filter/AllPassFilter.java | 41 -
.../variantcontext/filter/CompoundFilterTest.java | 78 -
.../FilteringVariantContextIteratorTest.java | 88 -
.../filter/GenotypeQualityFilterTest.java | 105 -
.../filter/HeterozygosityFilterTest.java | 128 -
.../filter/JavascriptVariantFilterTest.java | 72 -
.../filter/PassingVariantFilterTest.java | 46 -
.../variantcontext/filter/SnpFilterTest.java | 54 -
.../writer/TabixOnTheFlyIndexCreationTest.java | 66 -
.../variantcontext/writer/VCFWriterUnitTest.java | 280 -
.../VariantContextWriterBuilderUnitTest.java | 399 -
.../writer/VariantContextWritersUnitTest.java | 163 -
.../htsjdk/variant/vcf/AbstractVCFCodecTest.java | 60 -
.../htsjdk/variant/vcf/IndexFactoryUnitTest.java | 96 -
.../variant/vcf/VCFCompoundHeaderLineUnitTest.java | 46 -
.../java/htsjdk/variant/vcf/VCFEncoderTest.java | 125 -
.../vcf/VCFHeaderLineTranslatorUnitTest.java | 62 -
.../htsjdk/variant/vcf/VCFHeaderLineUnitTest.java | 43 -
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 563 -
.../vcf/VCFStandardHeaderLinesUnitTest.java | 204 -
.../BAMCigarOverflowTest/CigarOverflowTest.bam | Bin 662 -> 0 bytes
.../samtools/BAMFileIndexTest/index_test.bam | Bin 594149 -> 0 bytes
.../samtools/BAMFileIndexTest/index_test.bam.bai | Bin 1621416 -> 0 bytes
.../BAMFileIndexTest/symlink_with_index.bam | 1 -
.../BAMFileIndexTest/symlink_with_index.bam.bai | 1 -
.../symlink_without_linked_index.bam | 1 -
.../SAMIntegerTagTest/variousAttributes.bam | Bin 258 -> 0 bytes
.../SAMIntegerTagTest/variousAttributes.sam | 4 -
.../SamFileHeaderMergerTest/Chromosome1to10.bam | Bin 3708 -> 0 bytes
.../SamFileHeaderMergerTest/Chromosome5to9.bam | Bin 1991 -> 0 bytes
.../case1/chr11sub_file1.sam | 5 -
.../case1/chr11sub_file2.sam | 11 -
.../case1/expected_output.sam | 13 -
.../case2/chr11sub_file1.sam | 9 -
.../case2/chr11sub_file2.sam | 7 -
.../case2/chr11sub_file3.sam | 9 -
.../case2/chr11sub_file4.sam | 5 -
.../case2/expected_output.sam | 21 -
.../SamFileHeaderMergerTest/unsorted_input/1.sam | 11 -
.../SamFileHeaderMergerTest/unsorted_input/2.sam | 11 -
.../reference_with_lower_and_uppercase.dict | 3 -
.../reference_with_lower_and_uppercase.fasta | 4 -
.../reference_with_lower_and_uppercase.fasta.fai | 2 -
.../SequenceUtil/upper_and_lowercase_read.sam | 10 -
.../samtools/ValidateSamFileTest/bad_index.bai | Bin 1621416 -> 0 bytes
.../samtools/ValidateSamFileTest/bad_index.bam | Bin 594149 -> 0 bytes
.../samtools/ValidateSamFileTest/buggyHeader.sam | 30 -
.../samtools/ValidateSamFileTest/duplicate_rg.sam | 11 -
.../ValidateSamFileTest/duplicated_reads.sam | 17 -
.../duplicated_reads_out_of_order.sam | 17 -
.../samtools/ValidateSamFileTest/hanging_tab.sam | 3 -
.../inappropriate_mate_cigar_string.sam | 13 -
.../invalid_coord_sort_order.sam | 27 -
.../invalid_mate_cigar_string.sam | 19 -
.../ValidateSamFileTest/invalid_platform_unit.sam | 21 -
.../invalid_queryname_sort_order.sam | 27 -
.../ValidateSamFileTest/mate_cigar_and_no_oqs.sam | 4 -
.../ValidateSamFileTest/mate_cigar_and_oqs.sam | 4 -
.../ValidateSamFileTest/missing_fields.sam | 3 -
.../ValidateSamFileTest/missing_platform_unit.sam | 10 -
.../test_samfile_version_1pt5.bam | Bin 259 -> 0 bytes
.../samtools/ValidateSamFileTest/truncated.bam | Bin 336031 -> 0 bytes
.../ValidateSamFileTest/truncated_quals.sam | 4 -
.../samtools/ValidateSamFileTest/truncated_tag.sam | 4 -
.../htsjdk/samtools/ValidateSamFileTest/valid.sam | 21 -
.../ValidateSamFileTest/zero_length_read.sam | 3 -
.../htsjdk/samtools/block_compressed.sam.gz | Bin 257 -> 0 bytes
src/test/resources/htsjdk/samtools/compressed.bam | Bin 307 -> 0 bytes
.../resources/htsjdk/samtools/compressed.sam.gz | Bin 238 -> 0 bytes
.../htsjdk/samtools/coordinate_sorted.sam | 15 -
.../cram/CRAMException/testContigNotInRef.cram | Bin 3433 -> 0 bytes
.../cram/CRAMException/testContigNotInRef.cram.bai | Bin 96 -> 0 bytes
.../cram/CRAMException/testContigNotInRef.dict | 2 -
.../cram/CRAMException/testContigNotInRef.fa | 2 -
.../cram/CRAMException/testContigNotInRef.fa.fai | 1 -
.../cram/CRAMException/testContigNotInRef.fasta | 2 -
...78.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram | Bin 47259 -> 0 bytes
....21.1-100.100-SeqsPerSlice.0-unMapped.cram.crai | Bin 81 -> 0 bytes
...78.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram | Bin 47796 -> 0 bytes
....21.1-100.100-SeqsPerSlice.1-unMapped.cram.crai | Bin 94 -> 0 bytes
....20.21.1-100.100-SeqsPerSlice.500-unMapped.cram | Bin 77664 -> 0 bytes
...1.1-100.100-SeqsPerSlice.500-unMapped.cram.crai | Bin 124 -> 0 bytes
.../htsjdk/samtools/cram/auxf#values.2.1.cram | Bin 11427 -> 0 bytes
.../htsjdk/samtools/cram/auxf#values.3.0.cram | Bin 1586 -> 0 bytes
.../resources/htsjdk/samtools/cram/auxf#values.sam | 5 -
.../htsjdk/samtools/cram/auxf.alteredForMD5test.fa | 2 -
.../samtools/cram/auxf.alteredForMD5test.fa.fai | 1 -
src/test/resources/htsjdk/samtools/cram/auxf.fa | 2 -
.../resources/htsjdk/samtools/cram/auxf.fa.fai | 1 -
.../htsjdk/samtools/cram/c1#bounds.2.1.cram | Bin 10508 -> 0 bytes
.../htsjdk/samtools/cram/c1#bounds.3.0.cram | Bin 642 -> 0 bytes
.../resources/htsjdk/samtools/cram/c1#bounds.sam | 4 -
.../htsjdk/samtools/cram/c1#clip.2.1.cram | Bin 10630 -> 0 bytes
.../htsjdk/samtools/cram/c1#clip.3.0.cram | Bin 771 -> 0 bytes
.../resources/htsjdk/samtools/cram/c1#clip.sam | 8 -
.../htsjdk/samtools/cram/c1#noseq.2.1.cram | Bin 10652 -> 0 bytes
.../htsjdk/samtools/cram/c1#noseq.3.0.cram | Bin 797 -> 0 bytes
.../resources/htsjdk/samtools/cram/c1#noseq.sam | 10 -
.../htsjdk/samtools/cram/c1#pad1.2.1.cram | Bin 10623 -> 0 bytes
.../htsjdk/samtools/cram/c1#pad1.3.0.cram | Bin 761 -> 0 bytes
.../resources/htsjdk/samtools/cram/c1#pad1.sam | 10 -
.../htsjdk/samtools/cram/c1#pad2.2.1.cram | Bin 10658 -> 0 bytes
.../htsjdk/samtools/cram/c1#pad2.3.0.cram | Bin 796 -> 0 bytes
.../resources/htsjdk/samtools/cram/c1#pad2.sam | 14 -
.../htsjdk/samtools/cram/c1#pad3.2.1.cram | Bin 10697 -> 0 bytes
.../htsjdk/samtools/cram/c1#pad3.3.0.cram | Bin 848 -> 0 bytes
.../resources/htsjdk/samtools/cram/c1#pad3.sam | 14 -
.../htsjdk/samtools/cram/c1#unknown.2.1.cram | Bin 10784 -> 0 bytes
.../htsjdk/samtools/cram/c1#unknown.3.0.cram | Bin 949 -> 0 bytes
.../resources/htsjdk/samtools/cram/c1#unknown.sam | 9 -
src/test/resources/htsjdk/samtools/cram/c1.fa | 2 -
src/test/resources/htsjdk/samtools/cram/c1.fa.fai | 1 -
.../resources/htsjdk/samtools/cram/c2#pad.2.1.cram | Bin 11077 -> 0 bytes
.../resources/htsjdk/samtools/cram/c2#pad.3.0.cram | Bin 1070 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#1.2.1.cram | Bin 10746 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#1.3.0.cram | Bin 895 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/ce#1.sam | 2 -
.../resources/htsjdk/samtools/cram/ce#2.2.1.cram | Bin 10839 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#2.3.0.cram | Bin 988 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/ce#2.sam | 3 -
.../resources/htsjdk/samtools/cram/ce#5.2.1.cram | Bin 11221 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#5.3.0.cram | Bin 1130 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/ce#5.sam | 11 -
.../resources/htsjdk/samtools/cram/ce#5b.2.1.cram | Bin 12668 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#5b.3.0.cram | Bin 2669 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/ce#5b.sam | 12 -
.../htsjdk/samtools/cram/ce#large_seq.2.1.cram | Bin 101355 -> 0 bytes
.../htsjdk/samtools/cram/ce#large_seq.3.0.cram | Bin 84800 -> 0 bytes
.../htsjdk/samtools/cram/ce#large_seq.sam | 3 -
.../htsjdk/samtools/cram/ce#supp.2.1.cram | Bin 10649 -> 0 bytes
.../htsjdk/samtools/cram/ce#supp.3.0.cram | Bin 809 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#supp.sam | 6 -
.../htsjdk/samtools/cram/ce#tag_depadded.2.1.cram | Bin 11114 -> 0 bytes
.../htsjdk/samtools/cram/ce#tag_depadded.3.0.cram | Bin 1258 -> 0 bytes
.../htsjdk/samtools/cram/ce#tag_depadded.sam | 11 -
.../htsjdk/samtools/cram/ce#tag_padded.2.1.cram | Bin 10922 -> 0 bytes
.../htsjdk/samtools/cram/ce#tag_padded.3.0.cram | Bin 1082 -> 0 bytes
.../htsjdk/samtools/cram/ce#tag_padded.sam | 11 -
.../htsjdk/samtools/cram/ce#unmap.2.1.cram | Bin 10503 -> 0 bytes
.../htsjdk/samtools/cram/ce#unmap.3.0.cram | Bin 601 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#unmap.sam | 6 -
.../htsjdk/samtools/cram/ce#unmap1.2.1.cram | Bin 11730 -> 0 bytes
.../htsjdk/samtools/cram/ce#unmap1.3.0.cram | Bin 1505 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#unmap1.sam | 20 -
.../htsjdk/samtools/cram/ce#unmap2.2.1.cram | Bin 12587 -> 0 bytes
.../htsjdk/samtools/cram/ce#unmap2.3.0.cram | Bin 2404 -> 0 bytes
.../resources/htsjdk/samtools/cram/ce#unmap2.sam | 29 -
src/test/resources/htsjdk/samtools/cram/ce.fa | 20803 -------------
src/test/resources/htsjdk/samtools/cram/ce.fa.fai | 7 -
.../htsjdk/samtools/cram/cramQueryTest.cram | Bin 2863 -> 0 bytes
.../htsjdk/samtools/cram/cramQueryTest.cram.bai | Bin 336 -> 0 bytes
.../htsjdk/samtools/cram/cramQueryTestEmpty.cram | Bin 2183 -> 0 bytes
.../samtools/cram/cramQueryTestEmpty.cram.bai | Bin 48 -> 0 bytes
.../htsjdk/samtools/cram/cramQueryWithBAI.cram | Bin 8947 -> 0 bytes
.../htsjdk/samtools/cram/cramQueryWithBAI.cram.bai | Bin 152 -> 0 bytes
.../htsjdk/samtools/cram/cramQueryWithCRAI.cram | Bin 4131 -> 0 bytes
.../samtools/cram/cramQueryWithCRAI.cram.crai | Bin 59 -> 0 bytes
.../resources/htsjdk/samtools/cram/fieldarith.sam | 15 -
.../samtools/cram/human_g1k_v37.20.21.1-100.dict | 3 -
.../samtools/cram/human_g1k_v37.20.21.1-100.fasta | 11 -
.../cram/human_g1k_v37.20.21.1-100.fasta.fai | 2 -
.../cram/human_g1k_v37.20.21.10M-10M200k.dict | 3 -
.../cram/human_g1k_v37.20.21.10M-10M200k.fasta | 5002 ---
.../cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai | 2 -
.../htsjdk/samtools/cram/io/bzip2-test.bz2 | Bin 56 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/test.cram | Bin 3433 -> 0 bytes
.../resources/htsjdk/samtools/cram/test.cram.bai | Bin 96 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/test.dict | 2 -
src/test/resources/htsjdk/samtools/cram/test.fa | 2 -
.../resources/htsjdk/samtools/cram/test.fa.fai | 1 -
src/test/resources/htsjdk/samtools/cram/test2.cram | Bin 3433 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/test2.dict | 2 -
src/test/resources/htsjdk/samtools/cram/test2.fa | 2 -
.../resources/htsjdk/samtools/cram/test2.fa.fai | 1 -
.../htsjdk/samtools/cram/xx#blank.2.1.cram | Bin 10080 -> 0 bytes
.../htsjdk/samtools/cram/xx#blank.3.0.cram | Bin 140 -> 0 bytes
.../htsjdk/samtools/cram/xx#large_aux.2.1.cram | Bin 35824 -> 0 bytes
.../htsjdk/samtools/cram/xx#large_aux.3.0.cram | Bin 20418 -> 0 bytes
.../htsjdk/samtools/cram/xx#large_aux.sam | 4 -
.../htsjdk/samtools/cram/xx#large_aux2.2.1.cram | Bin 10868 -> 0 bytes
.../htsjdk/samtools/cram/xx#large_aux2.3.0.cram | Bin 1008 -> 0 bytes
.../htsjdk/samtools/cram/xx#large_aux2.sam | 11 -
.../htsjdk/samtools/cram/xx#minimal.2.1.cram | Bin 10995 -> 0 bytes
.../htsjdk/samtools/cram/xx#minimal.3.0.cram | Bin 1096 -> 0 bytes
.../resources/htsjdk/samtools/cram/xx#minimal.sam | 10 -
.../htsjdk/samtools/cram/xx#pair.2.1.cram | Bin 10454 -> 0 bytes
.../htsjdk/samtools/cram/xx#pair.3.0.cram | Bin 590 -> 0 bytes
.../resources/htsjdk/samtools/cram/xx#pair.sam | 7 -
.../resources/htsjdk/samtools/cram/xx#rg.2.1.cram | Bin 10643 -> 0 bytes
.../resources/htsjdk/samtools/cram/xx#rg.3.0.cram | Bin 794 -> 0 bytes
src/test/resources/htsjdk/samtools/cram/xx#rg.sam | 13 -
.../htsjdk/samtools/cram/xx#tlen.2.1.cram | Bin 11312 -> 0 bytes
.../htsjdk/samtools/cram/xx#tlen.3.0.cram | Bin 1296 -> 0 bytes
.../htsjdk/samtools/cram/xx#tlen2.2.1.cram | Bin 11380 -> 0 bytes
.../htsjdk/samtools/cram/xx#tlen2.3.0.cram | Bin 1359 -> 0 bytes
.../htsjdk/samtools/cram/xx#triplet.2.1.cram | Bin 10853 -> 0 bytes
.../htsjdk/samtools/cram/xx#triplet.3.0.cram | Bin 950 -> 0 bytes
.../resources/htsjdk/samtools/cram/xx#triplet.sam | 7 -
.../htsjdk/samtools/cram/xx#unsorted.2.1.cram | Bin 11131 -> 0 bytes
.../htsjdk/samtools/cram/xx#unsorted.3.0.cram | Bin 1262 -> 0 bytes
.../resources/htsjdk/samtools/cram/xx#unsorted.sam | 8 -
src/test/resources/htsjdk/samtools/cram/xx.fa | 5 -
src/test/resources/htsjdk/samtools/cram/xx.fa.fai | 2 -
.../htsjdk/samtools/cram_query_sorted.cram | Bin 13266 -> 0 bytes
.../htsjdk/samtools/cram_query_sorted.fasta | 40 -
.../htsjdk/samtools/cram_query_sorted.fasta.fai | 8 -
src/test/resources/htsjdk/samtools/cram_tlen.fasta | 41 -
.../resources/htsjdk/samtools/cram_tlen.fasta.fai | 8 -
.../htsjdk/samtools/cram_tlen_reads.sorted.sam | 19 -
.../htsjdk/samtools/cram_with_bai_index.cram | Bin 4213 -> 0 bytes
.../htsjdk/samtools/cram_with_bai_index.cram.bai | Bin 336 -> 0 bytes
.../htsjdk/samtools/cram_with_crai_index.cram | Bin 4213 -> 0 bytes
.../htsjdk/samtools/cram_with_crai_index.cram.crai | Bin 77 -> 0 bytes
src/test/resources/htsjdk/samtools/empty.bai | Bin 8 -> 0 bytes
src/test/resources/htsjdk/samtools/empty.bam | Bin 90 -> 0 bytes
.../htsjdk/samtools/empty_no_empty_gzip_block.bai | Bin 8 -> 0 bytes
.../htsjdk/samtools/empty_no_empty_gzip_block.bam | Bin 62 -> 0 bytes
src/test/resources/htsjdk/samtools/hg19mini.dict | 5 -
src/test/resources/htsjdk/samtools/hg19mini.fasta | 804 -
.../resources/htsjdk/samtools/hg19mini.fasta.fai | 4 -
.../intervallist/IntervalListFromVCFTest.vcf | 53 -
.../IntervalListFromVCFTestComp.interval_list | 7 -
...ntervalListFromVCFTestCompInverse.interval_list | 10 -
...lListFromVCFTestCompInverseManual.interval_list | 10 -
.../intervallist/IntervalListFromVCFTestManual.vcf | 57 -
...IntervalListFromVCFTestManualComp.interval_list | 12 -
.../IntervalListchr123_empty.interval_list | 4 -
src/test/resources/htsjdk/samtools/inttest.bam | Bin 329 -> 0 bytes
src/test/resources/htsjdk/samtools/inttest.sam | 26 -
.../resources/htsjdk/samtools/io/5newline5.txt | 2 -
.../resources/htsjdk/samtools/io/slurptest.txt | 3 -
src/test/resources/htsjdk/samtools/issue76.bam | Bin 5121 -> 0 bytes
src/test/resources/htsjdk/samtools/issue76.bam.bai | Bin 776 -> 0 bytes
.../htsjdk/samtools/liftover/hg18ToHg19.over.chain | 30850 -------------------
.../htsjdk/samtools/metrics/metricsOne.metrics | 13 -
.../htsjdk/samtools/metrics/metricsOneCopy.metrics | 13 -
.../metrics/metricsOneModifiedHistogram.metrics | 14 -
.../metrics/metricsOneModifiedMetrics.metrics | 13 -
.../resources/htsjdk/samtools/queryname_sorted.sam | 15 -
.../resources/htsjdk/samtools/readWithBadRname.sam | 6 -
.../reference/Homo_sapiens_assembly18.fasta.fai | 45 -
.../reference/Homo_sapiens_assembly18.trimmed.dict | 3 -
.../Homo_sapiens_assembly18.trimmed.fasta | 16946 ----------
.../Homo_sapiens_assembly18.trimmed.fasta.fai | 2 -
.../Homo_sapiens_assembly18.trimmed.nodict.fasta | 16946 ----------
...omo_sapiens_assembly18.trimmed.nodict.fasta.fai | 2 -
.../Homo_sapiens_assembly18.trimmed.noindex.fasta | 16946 ----------
.../reference_with_trailing_whitespace.dict | 3 -
.../reference_with_trailing_whitespace.fasta | 4 -
.../htsjdk/samtools/reference/testing.fai | 7 -
src/test/resources/htsjdk/samtools/roundtrip.sam | 16 -
src/test/resources/htsjdk/samtools/samFilter01.js | 2 -
src/test/resources/htsjdk/samtools/samFilter02.js | 9 -
.../samtools/seekablestream/megabyteZeros.dat | Bin 1000000 -> 0 bytes
.../htsjdk/samtools/seekablestream/seekTest.txt | 5 -
.../htsjdk/samtools/sequenceWithSpace.bam | Bin 391 -> 0 bytes
.../htsjdk/samtools/sequenceWithSpace.sam | 6 -
.../htsjdk/samtools/serialization_test.bam | Bin 339 -> 0 bytes
.../htsjdk/samtools/serialization_test.bam.bai | Bin 120 -> 0 bytes
.../htsjdk/samtools/serialization_test.sam | 8 -
.../resources/htsjdk/samtools/sra/test_archive.sra | Bin 1099831 -> 0 bytes
.../resources/htsjdk/samtools/uncompressed.sam | 15 -
src/test/resources/htsjdk/samtools/unsorted.sam | 15 -
.../5k-30BB2AAXX.3.aligned.sam.fastq | 19808 ------------
.../illumina-as-standard.bam | Bin 652 -> 0 bytes
.../QualityEncodingDetectorTest/s_1_sequence.txt | 40 -
.../solexa-as-standard.bam | Bin 944 -> 0 bytes
.../solexa_full_range_as_solexa.fastq | 8 -
.../util/QualityEncodingDetectorTest/unmapped.sam | 12 -
.../htsjdk/samtools/util/defective_bgzf.bam | Bin 359 -> 0 bytes
.../htsjdk/samtools/util/no_bgzf_terminator.bam | Bin 354 -> 0 bytes
.../htsjdk/samtools/util/whitespace_text_file.txt | 6 -
src/test/resources/htsjdk/tribble/Tb.vcf.idx | Bin 998966 -> 0 bytes
src/test/resources/htsjdk/tribble/basicDbSNP.dbsnp | 43 -
....deletions.10kbp.het.gq99.hand_curated.hg19.bed | 35 -
...ions.10kbp.het.gq99.hand_curated.hg19_fixed.bed | 36 -
.../htsjdk/tribble/bed/Unigene.sample.bed | 72 -
.../resources/htsjdk/tribble/bed/disconcontigs.bed | 5 -
src/test/resources/htsjdk/tribble/bed/unsorted.bed | 5 -
.../resources/htsjdk/tribble/complexExample.vcf | 23 -
src/test/resources/htsjdk/tribble/fakeBed.bed | 51 -
src/test/resources/htsjdk/tribble/fakeVCF.vcf.gz | Bin 351859 -> 0 bytes
.../resources/htsjdk/tribble/fakeVCF.vcf.gz.tbi | Bin 170 -> 0 bytes
src/test/resources/htsjdk/tribble/gwas/smallp.gwas | 20 -
.../htsjdk/tribble/index/chrY_Y4_small.bed | 5000 ---
src/test/resources/htsjdk/tribble/large.txt | 165 -
src/test/resources/htsjdk/tribble/sites.bed | 1000 -
src/test/resources/htsjdk/tribble/soapsnp.txt | 24 -
.../resources/htsjdk/tribble/split/test.bin.part1 | Bin 16000 -> 0 bytes
.../resources/htsjdk/tribble/split/test.bin.part2 | Bin 16000 -> 0 bytes
.../resources/htsjdk/tribble/split/test.bin.part3 | Bin 16000 -> 0 bytes
.../resources/htsjdk/tribble/split/test.bin.split | 3 -
.../tabix/YRI.trio.2010_07.indel.sites.vcf.gz | Bin 250626 -> 0 bytes
.../tabix/YRI.trio.2010_07.indel.sites.vcf.gz.tbi | Bin 32877 -> 0 bytes
.../htsjdk/tribble/tabix/bigger.vcf.gz.tbi | Bin 595996 -> 0 bytes
.../htsjdk/tribble/tabix/testTabixIndex.vcf | 51 -
.../htsjdk/tribble/tabix/testTabixIndex.vcf.gz | Bin 372 -> 0 bytes
.../resources/htsjdk/tribble/tabix/trioDup.vcf | 75 -
.../resources/htsjdk/tribble/tabix/trioDup.vcf.gz | Bin 1353 -> 0 bytes
.../htsjdk/tribble/tabix/trioDup.vcf.gz.tbi | Bin 324 -> 0 bytes
.../resources/htsjdk/tribble/test with spaces.vcf | 24 -
src/test/resources/htsjdk/tribble/test.bed | 9 -
src/test/resources/htsjdk/tribble/test.gff | 9 -
.../resources/htsjdk/tribble/test.tabix.bed.gz | Bin 116 -> 0 bytes
.../resources/htsjdk/tribble/test.tabix.bed.gz.tbi | Bin 121 -> 0 bytes
src/test/resources/htsjdk/tribble/test.vcf | 24 -
src/test/resources/htsjdk/tribble/test.vcf.bgz | Bin 849 -> 0 bytes
src/test/resources/htsjdk/tribble/test.vcf.gz | Bin 822 -> 0 bytes
src/test/resources/htsjdk/tribble/testGeliText.txt | 50 -
.../resources/htsjdk/tribble/testIntervalList.list | 6 -
src/test/resources/htsjdk/tribble/trio.vcf | 100 -
src/test/resources/htsjdk/tribble/trio.vcf.idx | Bin 495 -> 0 bytes
src/test/resources/htsjdk/tribble/trioDup.vcf | 75 -
src/test/resources/htsjdk/tribble/vcfexample.vcf | 12 -
.../resources/htsjdk/tribble/vcfexample.vcf.gz | Bin 471 -> 0 bytes
.../resources/htsjdk/tribble/vcfexample.vcf.gz.tbi | Bin 114 -> 0 bytes
.../htsjdk/tribble/vcfexample.vcf.truncated.gz | Bin 470 -> 0 bytes
.../htsjdk/tribble/vcfexample.vcf.truncated.hdr.gz | Bin 460 -> 0 bytes
src/test/resources/htsjdk/variant/HiSeq.10000.vcf | 10001 ------
...baseline.20111114.both.exome.genotypes.1000.vcf | 249 -
.../resources/htsjdk/variant/VCF4HeaderTest.vcf | 42 -
.../resources/htsjdk/variant/VQSR.mixedTest.recal | 32 -
src/test/resources/htsjdk/variant/breakpoint.vcf | 6 -
.../htsjdk/variant/dbsnp_135.b37.1000.vcf | 249 -
.../htsjdk/variant/diagnosis_targets_testfile.vcf | 117 -
src/test/resources/htsjdk/variant/ex2.bgzf.bcf.csi | Bin 130 -> 0 bytes
src/test/resources/htsjdk/variant/ex2.vcf | 23 -
.../htsjdk/variant/serialization_test.bcf | Bin 7490 -> 0 bytes
.../htsjdk/variant/serialization_test.bcf.idx | Bin 1146 -> 0 bytes
.../htsjdk/variant/structuralvariants.vcf | 22 -
.../Homo_sapiens_assembly18.trimmed.dict | 3 -
.../Homo_sapiens_assembly18.trimmed.fasta | 16946 ----------
.../Homo_sapiens_assembly18.trimmed.fasta.fai | 2 -
.../ScreenSamReads.100.input.sam | 21 -
.../empty.interval_list | 4 -
.../SamSequenceDictionaryExtractor/test1.dict | 3 -
.../utils/SamSequenceDictionaryExtractor/test1.vcf | 53 -
.../SamSequenceDictionaryExtractor/test1.vcf.idx | Bin 2283 -> 0 bytes
.../test1_comp.interval_list | 8 -
.../test2_comp.interval_list | 7 -
.../test3_comp.interval_list | 24 -
.../test4_comp.interval_list | 25 -
.../resources/htsjdk/variant/variantFilter01.js | 2 -
.../resources/htsjdk/variant/variantFilter02.js | 20 -
.../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl | Bin 2004 -> 0 bytes
.../Intensities/BaseCalls/L001/s_1_1101.filter | Bin 2012 -> 0 bytes
.../125T125T/Data/Intensities/L001/s_1_1101.clocs | Bin 4359 -> 0 bytes
.../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl | Bin 64 -> 0 bytes
.../Intensities/BaseCalls/L001/s_1_1101.filter | Bin 72 -> 0 bytes
.../sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam | 6 -
.../sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam | 14 -
.../sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam | 12 -
.../net/sf/picard/illumina/25T8B25T/sams/N.sam | 34 -
.../sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam | 6 -
.../sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam | 8 -
src/test/resources/testng.xml | 20 -
test/Makefile | 70 +
test/align/Makefile | 56 +
test/align/indextest.cpp | 113 +
test/cc/Makefile | 60 +
test/cc/asm-test.cpp | 480 +
test/cipher/Makefile | 52 +
test/cipher/test.sh | 46 +
test/judy_test/Makefile | 58 +
test/judy_test/judytest.c | 1831 ++
test/junit-4.11.jar | Bin 0 -> 288666 bytes
test/kapp/Makefile | 169 +
test/kapp/env-test-tool.c | 170 +
test/kapp/kapp-test.cpp | 549 +
test/kapp/qfiletest.c | 338 +
test/kapp/queuefile.data | 338 +
test/kapp/report-kns-agent.c | 58 +
test/kapp/run-kns-agent.sh | 60 +
test/kapp/run-sig-core.sh | 116 +
test/kapp/sig-core.c | 101 +
test/kdb/Makefile | 124 +
test/kdb/kdbtest.cpp | 183 +
test/kdb/remote_open_test.cpp | 304 +
test/kdb/root/sra/SRR000123.sra.cache | Bin 0 -> 2975732 bytes
test/kdb/rowsettest.cpp | 819 +
test/kdb/test-btree.c | 338 +
.../kdb/testdb/tbl/SEQUENCE/col/dummy | 0
test/kdb/wkdbtest.cpp | 264 +
test/kfc/Makefile | 57 +
test/kfc/kfc.c | 29 +
test/kfc/test-except.c | 133 +
test/kfg/Makefile | 139 +
test/kfg/config.linux.kfg | 26 +
test/kfg/config.schema.kfg | 25 +
test/kfg/config.sra.kfg | 29 +
test/kfg/flat-sra-kfg.cpp | 429 +
test/kfg/flat-sra-kfg/aux_root/empty.kfg | 1 +
test/kfg/flat-sra-kfg/new/sraFlat.kfg | 1 +
test/kfg/flat-sra-kfg/old/fuse1000.kfg | 1 +
test/kfg/keystoretest.cpp | 429 +
test/kfg/kfgtest.cpp | 1030 +
test/kfg/ncbi-home-from-env.configs/dir1/file.kfg | 2 +
.../dir1/not-user-settings.xml | 2 +
.../dir1/user-settings.mkfg | 2 +
test/kfg/ncbi-home-from-env.configs/dir2/file.kfg | 2 +
.../dir2/not-user-settings.xml | 2 +
.../dir2/user-settings.mkfg | 2 +
test/kfg/ncbi-home-from-env.cpp | 50 +
test/kfg/prj_2956.ngc | Bin 0 -> 91 bytes
test/kfg/repositorytest.cpp | 280 +
test/kfg/wb-test-kfg.cpp | 628 +
test/kfs/Makefile | 137 +
test/kfs/cacheteetest.cpp | 603 +
test/kfs/kfstest.cpp | 198 +
test/kfs/md5test.cpp | 199 +
test/kfs/ramfiletest.cpp | 199 +
test/kfs/resolvetest.cpp | 196 +
test/kfs/test.tar | Bin 0 -> 20480 bytes
test/klib/Makefile | 198 +
test/klib/asm-test.c | 114 +
test/klib/md5appendtest.c | 274 +
test/klib/printf-test.c | 836 +
test/klib/test-SraReleaseVersion.cpp | 316 +
test/klib/test-klib.cpp | 1027 +
test/klib/test-log.cpp | 317 +
test/klib/test-out.cpp | 156 +
test/klib/test-vnamelist.cpp | 364 +
test/kns/KNSManagerSingletonTest.cpp | 69 +
test/kns/Makefile | 172 +
test/kns/TestProxy.hpp | 227 +
test/kns/http-client.c | 17 +
test/kns/http-test.c | 368 +
test/kns/http_dropconnection_test.cpp | 437 +
test/kns/httptest.cpp | 875 +
test/kns/knstest.cpp | 1095 +
test/kns/nih_1_out.txt | 277 +
test/kns/test-proxy-with-env.cpp | 112 +
test/kns/test-proxy.cpp | 263 +
test/kns/test-proxy.h | 7 +
test/kns/test-proxy/2-path-no-env/config | 1 +
test/kns/test-proxy/2-path-no-env/expected | 2 +
test/kns/test-proxy/2-path-no-port-no-env/config | 1 +
test/kns/test-proxy/2-path-no-port-no-env/expected | 2 +
.../MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/config | 1 +
.../all.MULTIPLE_PROXIES/environment | 4 +
.../MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/expected | 10 +
.../disabled.MULTIPLE_PROXIES/config | 2 +
.../disabled.MULTIPLE_PROXIES/environment | 4 +
.../disabled.MULTIPLE_PROXIES/expected | 0
.../enabled.MULTIPLE_PROXIES/config | 2 +
.../enabled.MULTIPLE_PROXIES/environment | 4 +
.../enabled.MULTIPLE_PROXIES/expected | 10 +
.../env-kfg.MULTIPLE_PROXIES/config | 2 +
.../env-kfg.MULTIPLE_PROXIES/environment | 4 +
.../env-kfg.MULTIPLE_PROXIES/expected | 10 +
.../env-only.MULTIPLE_PROXIES/config | 2 +
.../env-only.MULTIPLE_PROXIES/environment | 4 +
.../env-only.MULTIPLE_PROXIES/expected | 8 +
.../ignore.MULTIPLE_PROXIES/config | 2 +
.../ignore.MULTIPLE_PROXIES/environment | 4 +
.../ignore.MULTIPLE_PROXIES/expected | 0
.../kfg-env.MULTIPLE_PROXIES/config | 2 +
.../kfg-env.MULTIPLE_PROXIES/environment | 4 +
.../kfg-env.MULTIPLE_PROXIES/expected | 10 +
.../proxy-not-only.MULTIPLE_PROXIES/config | 2 +
.../proxy-not-only.MULTIPLE_PROXIES/environment | 4 +
.../proxy-not-only.MULTIPLE_PROXIES/expected | 10 +
.../proxy-only.MILTIPLE_PROXIES/config | 2 +
.../proxy-only.MILTIPLE_PROXIES/environment | 4 +
.../proxy-only.MILTIPLE_PROXIES/expected | 10 +
test/kns/test-proxy/all/config | 1 +
test/kns/test-proxy/all/environment | 4 +
test/kns/test-proxy/all/expected | 5 +
test/kns/test-proxy/comma-error/environment | 1 +
.../kns/test-proxy/comma-error/expected | 0
test/kns/test-proxy/disabled/config | 2 +
test/kns/test-proxy/disabled/environment | 4 +
.../kns/test-proxy/disabled/expected | 0
test/kns/test-proxy/enabled/config | 2 +
test/kns/test-proxy/enabled/environment | 4 +
test/kns/test-proxy/enabled/expected | 5 +
test/kns/test-proxy/env-kfg/config | 2 +
test/kns/test-proxy/env-kfg/environment | 4 +
test/kns/test-proxy/env-kfg/expected | 5 +
test/kns/test-proxy/env-only/config | 2 +
test/kns/test-proxy/env-only/environment | 4 +
test/kns/test-proxy/env-only/expected | 4 +
test/kns/test-proxy/error/config | 1 +
test/kns/test-proxy/error/environment | 1 +
.../kns/test-proxy/error/expected | 0
test/kns/test-proxy/http_proxy/environment | 1 +
test/kns/test-proxy/http_proxy/expected | 1 +
test/kns/test-proxy/ignore/config | 2 +
test/kns/test-proxy/ignore/environment | 4 +
.../kns/test-proxy/ignore/expected | 0
test/kns/test-proxy/kfg-env/config | 2 +
test/kns/test-proxy/kfg-env/environment | 4 +
test/kns/test-proxy/kfg-env/expected | 5 +
test/kns/test-proxy/kfg-only/config | 2 +
test/kns/test-proxy/kfg-only/environment | 4 +
test/kns/test-proxy/kfg-only/expected | 1 +
test/kns/test-proxy/no-env/config | 1 +
test/kns/test-proxy/no-env/expected | 1 +
test/kns/test-proxy/no-port-no-env/config | 1 +
test/kns/test-proxy/no-port-no-env/expected | 1 +
test/kns/test-proxy/proxy-not-only/config | 2 +
test/kns/test-proxy/proxy-not-only/environment | 4 +
test/kns/test-proxy/proxy-not-only/expected | 5 +
test/kns/test-proxy/proxy-only/config | 2 +
test/kns/test-proxy/proxy-only/environment | 4 +
test/kns/test-proxy/proxy-only/expected | 5 +
test/kproc/Makefile | 55 +
test/kproc/kproctest.cpp | 1000 +
test/krypto/Makefile | 215 +
test/krypto/test-aes-ciphers.c | 792 +
test/krypto/test-cipher-speed.c | 910 +
test/krypto/test-cmn.cpp | 359 +
test/krypto/test-cmn.hpp | 90 +
test/krypto/test-csprng.c | 230 +
test/krypto/test-encdec.cpp | 607 +
test/krypto/test-krypto-slow.cpp | 401 +
test/krypto/test-modes.c | 1261 +
test/krypto/test-reenc.cpp | 376 +
test/ktst/Makefile | 60 +
test/ktst/ktsttest.cpp | 186 +
test/loader/Makefile | 58 +
test/loader/loadertest.cpp | 407 +
test/loader/sequence-writer.c | 366 +
test/loader/sequencewriter.vschema | 47 +
test/ngs-c++/CSRA1PileupTest.cpp | 742 +
test/ngs-c++/CSRA1_ReadCollection_test.cpp | 252 +
test/ngs-c++/CSRA1test.cpp | 1105 +
test/ngs-c++/Makefile | 139 +
test/ngs-c++/NGStest.cpp | 71 +
test/ngs-c++/SRADBtest.cpp | 536 +
test/ngs-c++/SRAtest.cpp | 478 +
test/ngs-c++/SRR600096 | Bin 0 -> 81253 bytes
test/ngs-c++/SRR611340 | Bin 0 -> 211261 bytes
test/ngs-c++/ngsfixture.hpp | 93 +
test/ngs-c++/seq_spot_id_0.sra | Bin 0 -> 14316329 bytes
test/ngs-c++/valgrind.suppress | 12 +
test/ngs-java/Makefile | 125 +
test/ngs-java/build.xml | 53 +
test/ngs-java/ngs_test_CSRA1.java | 963 +
test/ngs-java/ngs_test_lib_load.java | 246 +
test/ngs-python/Makefile | 57 +
test/ngs-python/build.xml | 41 +
test/ngs-python/tests.py | 506 +
test/ngs/Makefile | 216 +
test/ngs/data/.gitignore | 1 +
test/ngs/data/SysPathTest/md/cur | Bin 0 -> 21398 bytes
test/ngs/data/SysPathTest/md5 | 1 +
.../data/SysPathTest/tbl/SEQUENCE/col/READ/data | Bin 0 -> 143 bytes
.../ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/idx | Bin 0 -> 40 bytes
.../data/SysPathTest/tbl/SEQUENCE/col/READ/idx0 | 0
.../data/SysPathTest/tbl/SEQUENCE/col/READ/idx1 | Bin 0 -> 132 bytes
.../data/SysPathTest/tbl/SEQUENCE/col/READ/idx2 | Bin 0 -> 112 bytes
.../data/SysPathTest/tbl/SEQUENCE/col/READ/md/cur | Bin 0 -> 174 bytes
.../ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/md5 | 6 +
test/ngs/data/SysPathTest/tbl/SEQUENCE/md/cur | Bin 0 -> 21734 bytes
test/ngs/data/SysPathTest/tbl/SEQUENCE/md5 | 1 +
test/ngs/ngs_c_fixture.hpp | 180 +
test/ngs/ngstest.cpp | 956 +
test/ngs/ngstest_csra1.cpp | 1365 +
test/ngs/ngstest_csra1_pileup.cpp | 577 +
test/ngs/ngstest_csra1_readcollection.cpp | 739 +
test/ngs/ngstest_csra1_refwin.cpp | 824 +
test/ngs/ngstest_fragmentblob.cpp | 597 +
test/ngs/ngstest_makedb.cpp | 196 +
test/ngs/ngstest_reference.cpp | 158 +
test/ngs/ngstest_sra.cpp | 1071 +
test/ngs/ngstest_sradb.cpp | 866 +
test/ngs/valgrind.suppress | 16 +
test/only-remote-repository.kfg | 2 +
test/search/Makefile | 61 +
test/search/PerfCounter.h | 211 +
test/search/agrep-main.c | 346 +
test/search/search-vdb.cpp | 512 +
test/search/search-vdb.h | 229 +
test/search/test-agrep.cpp | 928 +
test/sraxf/Makefile | 60 +
test/sraxf/fix_read_seg-test.cpp | 131 +
test/vdb/.gitignore | 1 +
test/vdb/Makefile | 246 +
test/vdb/SYS-224064.cpp | 237 +
test/vdb/db/blob_val_inv_chsum.sra | Bin 0 -> 196213 bytes
test/vdb/kfg/empty/empty.kfg | 1 +
test/vdb/kfg/linux/test-dependencies.kfg | 3 +
test/vdb/test-VDB-3060.cpp | 411 +
test/vdb/test-VDB-3061.cpp | 250 +
test/vdb/test-blob-val.cpp | 185 +
test/vdb/test-dependencies.cpp | 452 +
test/vdb/test-sparse-col.cpp | 358 +
test/vdb/test-vdb.cpp | 624 +
test/vdb/test-wvdb.cpp | 520 +
test/vfs/Makefile | 141 +
test/vfs/caching-kfg/incomplete.kfg | 4 +
test/vfs/managertest.cpp | 490 +
test/vfs/ncbi/protected1/SRR999997 | 1 +
test/vfs/ncbi/protected1/SRR999997.ncbi_enc | Bin 0 -> 32864 bytes
.../vfs/ncbi/public/refseq/YYZZ99 | 0
.../vfs/ncbi/public/refseq/ZZ999999.9 | 0
.../vfs/ncbi/public/sra/SRR999998.sra | 0
.../.gitignore => test/vfs/ncbi/public/wgs/YYZZ99 | 0
test/vfs/ncbi_enc | Bin 0 -> 65696 bytes
test/vfs/path-test.c | 765 +
test/vfs/pathtest.cpp | 737 +
.../redirect-rejected-names-cgi-http-to-https.cpp | 213 +
.../incomplete.kfg | 1 +
.../vfs/repo/wgs/WGS/YY/ZZ/YYZZ10 | 0
.../vfs/repo/wgs/WGS/YY/ZZ/YYZZ99 | 0
.../vfs/repo/wgs2/WGS/YY/ZZ/YYZZ20 | 0
.../vfs/repo/wgs2/WGS/YY/ZZ/YYZZ99 | 0
test/vfs/resolvertest.cpp | 344 +
test/vfs/test-caching.cpp | 615 +
test/vxf/Makefile | 83 +
test/vxf/VDB-2915.cpp | 508 +
test/vxf/local_config/local.kfg | 2 +
test/vxf/wb-irzip-impl.c | 88 +
test/vxf/wb-irzip-impl.h | 56 +
test/vxf/wb-test-vxf.cpp | 268 +
vdb3/itf/kfc/array.hpp | 127 +
vdb3/itf/kfc/atomic-ia32.hpp | 500 +
vdb3/itf/kfc/atomic-x86_64.hpp | 356 +
vdb3/itf/kfc/atomic.hpp | 133 +
vdb3/itf/kfc/callstk.hpp | 117 +
vdb3/itf/kfc/caps.hpp | 59 +
vdb3/itf/kfc/defs.hpp | 113 +
vdb3/itf/kfc/except.hpp | 174 +
vdb3/itf/kfc/fd.hpp | 102 +
vdb3/itf/kfc/fdmgr.hpp | 95 +
vdb3/itf/kfc/integer.hpp | 191 +
vdb3/itf/kfc/log.hpp | 118 +
vdb3/itf/kfc/memmgr.hpp | 133 +
vdb3/itf/kfc/memory.hpp | 149 +
vdb3/itf/kfc/ptr.hpp | 174 +
vdb3/itf/kfc/ref.hpp | 155 +
vdb3/itf/kfc/refcount.hpp | 94 +
vdb3/itf/kfc/rsrc.hpp | 150 +
vdb3/itf/kfc/stream.hpp | 135 +
vdb3/itf/kfc/string.hpp | 252 +
vdb3/itf/kfc/syserr.hpp | 57 +
vdb3/itf/kfc/task-impl.hpp | 139 +
vdb3/itf/kfc/task.hpp | 124 +
vdb3/itf/kfc/time.hpp | 299 +
vdb3/itf/kfc/timemgr.hpp | 94 +
vdb3/itf/kfc/vers.hpp | 101 +
vdb3/src/kfc/Makefile | 88 +
vdb3/src/kfc/array.cpp | 152 +
vdb3/src/kfc/callstk.cpp | 60 +
vdb3/src/kfc/except.cpp | 222 +
vdb3/src/kfc/fd.cpp | 204 +
vdb3/src/kfc/fdmgr.cpp | 101 +
vdb3/src/kfc/integer.cpp | 137 +
vdb3/src/kfc/log.cpp | 142 +
vdb3/src/kfc/memmgr.cpp | 162 +
vdb3/src/kfc/memory.cpp | 392 +
vdb3/src/kfc/pfdmgr.cpp | 64 +
vdb3/src/kfc/pfdmgr.hpp | 68 +
vdb3/src/kfc/plogger.cpp | 148 +
vdb3/src/kfc/plogger.hpp | 72 +
vdb3/src/kfc/pmemmgr.cpp | 315 +
vdb3/src/kfc/pmemmgr.hpp | 75 +
vdb3/src/kfc/ptimemgr.cpp | 81 +
vdb3/src/kfc/ptimemgr.hpp | 64 +
vdb3/src/kfc/ptr.cpp | 206 +
vdb3/src/kfc/ref.cpp | 140 +
vdb3/src/kfc/refcount.cpp | 113 +
vdb3/src/kfc/rsrc.cpp | 141 +
vdb3/src/kfc/stream.cpp | 395 +
vdb3/src/kfc/string.cpp | 1324 +
vdb3/src/kfc/syserr.cpp | 97 +
vdb3/src/kfc/task-impl.cpp | 352 +
vdb3/src/kfc/task.cpp | 109 +
vdb3/src/kfc/time.cpp | 290 +
vdb3/src/kfc/timemgr.cpp | 105 +
vdb3/src/kfc/vers.cpp | 85 +
3014 files changed, 635632 insertions(+), 299493 deletions(-)
delete mode 100644 .github/ISSUE_TEMPLATE.md
delete mode 100644 .github/PULL_REQUEST_TEMPLATE.md
delete mode 100644 .travis.yml
create mode 100644 CHANGES.md
create mode 100644 LICENSE
create mode 100644 Makefile
delete mode 100644 build.gradle
delete mode 100755 build.xml
create mode 100644 build/.gitignore
create mode 100644 build/Makefile.cc
create mode 100644 build/Makefile.clang
create mode 100644 build/Makefile.env
create mode 100644 build/Makefile.gcc
create mode 100644 build/Makefile.icc
create mode 100644 build/Makefile.install
create mode 100644 build/Makefile.linux
create mode 100644 build/Makefile.rules
create mode 100644 build/Makefile.scm
create mode 100644 build/Makefile.shell
create mode 100644 build/Makefile.targets
create mode 100644 build/Makefile.vers
create mode 100755 build/abspath.sh
create mode 100755 build/cc.sh
create mode 100755 build/cp.sh
create mode 100755 build/gprof2dot.py
create mode 100755 build/increment-release.sh
create mode 100644 build/ld.linux.cmn.sh
create mode 100755 build/ld.linux.dlib.sh
create mode 100755 build/ld.linux.exe.sh
create mode 100644 build/ld.linux.exe_cmd.sh
create mode 100755 build/ld.linux.gcc.sh
create mode 100755 build/ld.linux.icc.sh
create mode 100755 build/ld.linux.ln.sh
create mode 100755 build/ld.linux.slib.sh
create mode 100755 build/ld.mac.clang.sh
create mode 100644 build/ld.mac.cmn.sh
create mode 100755 build/ld.mac.dlib.sh
create mode 100755 build/ld.mac.exe.sh
create mode 100755 build/ld.mac.gcc.sh
create mode 100755 build/ld.mac.ln.sh
create mode 100755 build/ld.mac.slib.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 100755 build/ld.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
create mode 100644 build/ld.unix.cmn.sh
create mode 100644 build/ld.unix.slib.sh
create mode 100755 build/ld.win.cmn.sh
create mode 100755 build/ld.win.dlib.sh
create mode 100755 build/ld.win.exe.sh
create mode 100755 build/ld.win.slib.sh
create mode 100755 build/ld.win.stub.sh
create mode 100755 build/ld.win.vc++.sh
create mode 100644 build/libexists.sh
create mode 100755 build/mac.arch.sh
create mode 100755 build/make-defs-xf.pl
create mode 100755 build/make-defs.pl
create mode 100755 build/make-vers-inc.sh
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/sra-dflt-schema.sh
create mode 100755 build/tag-module.sh
create mode 100644 build/valgrind.suppress
create mode 100755 build/wait_for_file.sh
create mode 100755 configure
delete mode 100644 gradle/wrapper/gradle-wrapper.jar
delete mode 100644 gradle/wrapper/gradle-wrapper.properties
delete mode 100755 gradlew
copy {src/main/java/htsjdk/tribble/util/ftp => interfaces}/.gitignore (100%)
create mode 100644 interfaces/align/align-access.h
create mode 100644 interfaces/align/align.h
create mode 100644 interfaces/align/align.vschema
create mode 100644 interfaces/align/alignsrc.h
create mode 100644 interfaces/align/bam.h
create mode 100644 interfaces/align/dna-reverse-cmpl.h
create mode 100644 interfaces/align/extern.h
create mode 100644 interfaces/align/iterator.h
create mode 100644 interfaces/align/iterator_examples.txt
create mode 100644 interfaces/align/manager.h
create mode 100644 interfaces/align/mate-cache.vschema
create mode 100644 interfaces/align/pileup-stats.vschema
create mode 100644 interfaces/align/qstat.vschema
create mode 100644 interfaces/align/quality-quantizer.h
create mode 100644 interfaces/align/reader-refseq.h
create mode 100644 interfaces/align/reference.h
create mode 100644 interfaces/align/refseq-mgr.h
create mode 100644 interfaces/align/refseq.vschema
create mode 100644 interfaces/align/seq.vschema
create mode 100644 interfaces/align/writer-alignment.h
create mode 100644 interfaces/align/writer-cmn.h
create mode 100644 interfaces/align/writer-reference.h
create mode 100644 interfaces/align/writer-refseq.h
create mode 100644 interfaces/align/writer-sequence.h
create mode 100644 interfaces/cc/cc/compiler.h
create mode 100644 interfaces/cc/gcc/compiler.h
create mode 100644 interfaces/cc/gcc/fat86/arch-impl.h
create mode 100644 interfaces/cc/gcc/fat86/atomic.h
create mode 100644 interfaces/cc/gcc/fat86/atomic32.h
create mode 100644 interfaces/cc/gcc/fat86/atomic64.h
create mode 100644 interfaces/cc/gcc/fat86/bitstr.h
create mode 100644 interfaces/cc/gcc/fat86/byteswap.h
create mode 100644 interfaces/cc/gcc/fat86/strtol.h
create mode 100644 interfaces/cc/gcc/i386/arch-impl.h
create mode 100644 interfaces/cc/gcc/i386/atomic.h
create mode 100644 interfaces/cc/gcc/i386/atomic32.h
create mode 100644 interfaces/cc/gcc/i386/bitstr.h
create mode 100644 interfaces/cc/gcc/i386/byteswap.h
create mode 100644 interfaces/cc/gcc/i386/strtol.h
create mode 100644 interfaces/cc/gcc/noarch/bitstr.h
create mode 100644 interfaces/cc/gcc/ppc32/arch-impl.h
create mode 100644 interfaces/cc/gcc/ppc32/atomic.h
create mode 100644 interfaces/cc/gcc/ppc32/atomic32.h
create mode 100644 interfaces/cc/gcc/ppc32/bitstr.h
create mode 100644 interfaces/cc/gcc/ppc32/strtol.h
create mode 100644 interfaces/cc/gcc/v128.h
create mode 100644 interfaces/cc/gcc/va_copy.h
create mode 100644 interfaces/cc/gcc/x86_64/arch-impl.h
create mode 100644 interfaces/cc/gcc/x86_64/atomic.h
create mode 100644 interfaces/cc/gcc/x86_64/atomic32.h
create mode 100644 interfaces/cc/gcc/x86_64/atomic64.h
create mode 100644 interfaces/cc/gcc/x86_64/bitstr.h
create mode 100644 interfaces/cc/gcc/x86_64/byteswap.h
create mode 100644 interfaces/cc/gcc/x86_64/strtol.h
create mode 100644 interfaces/cc/icc/compiler.h
create mode 100644 interfaces/cc/vc++/compiler.h
create mode 100644 interfaces/cc/vc++/i386/arch-impl.h
create mode 100644 interfaces/cc/vc++/i386/bitstr.h
create mode 100644 interfaces/cc/vc++/noarch/arch-impl.h
create mode 100644 interfaces/cc/vc++/noarch/bitstr.h
create mode 100644 interfaces/cc/vc++/stdbool.h
create mode 100644 interfaces/cc/vc++/stdint.h
create mode 100644 interfaces/cc/vc++/va_copy.h
create mode 100644 interfaces/cc/vc++/x86_64/arch-impl.h
create mode 100644 interfaces/cc/vc++/x86_64/bitstr.h
create mode 100644 interfaces/csra2/csra2.vschema
create mode 100644 interfaces/csra2/read.vschema
create mode 100644 interfaces/csra2/reference.vschema
create mode 100644 interfaces/csra2/stats.vschema
create mode 100644 interfaces/fastq/extern.h
create mode 100644 interfaces/fastq/fq-dump.h
create mode 100644 interfaces/hdf5/extern.h
create mode 100644 interfaces/hdf5/kdf5.h
create mode 100644 interfaces/insdc/insdc.h
create mode 100644 interfaces/insdc/insdc.vschema
create mode 100644 interfaces/insdc/seq.vschema
create mode 100644 interfaces/insdc/sra.h
create mode 100644 interfaces/insdc/sra.vschema
create mode 100644 interfaces/kapp/args-conv.h
create mode 100644 interfaces/kapp/args.h
create mode 100644 interfaces/kapp/extern.h
create mode 100644 interfaces/kapp/loader-file.h
create mode 100644 interfaces/kapp/loader-meta.h
create mode 100644 interfaces/kapp/log-xml.h
create mode 100644 interfaces/kapp/main.h
create mode 100644 interfaces/kapp/progressbar.h
create mode 100644 interfaces/kapp/queue-file.h
create mode 100644 interfaces/kdb/btree.h
create mode 100644 interfaces/kdb/column.h
create mode 100644 interfaces/kdb/consistency-check.h
create mode 100644 interfaces/kdb/database.h
create mode 100644 interfaces/kdb/extern.h
create mode 100644 interfaces/kdb/index.h
create mode 100644 interfaces/kdb/kdb-priv.h
create mode 100644 interfaces/kdb/manager.h
create mode 100644 interfaces/kdb/meta.h
create mode 100644 interfaces/kdb/meta.hpp
create mode 100644 interfaces/kdb/namelist.h
create mode 100644 interfaces/kdb/rowset-impl.h
create mode 100644 interfaces/kdb/rowset.h
create mode 100644 interfaces/kdb/table.h
create mode 100644 interfaces/kfc/callconv.h
create mode 100644 interfaces/kfc/ctx.h
create mode 100644 interfaces/kfc/defs.h
create mode 100644 interfaces/kfc/except.h
create mode 100644 interfaces/kfc/extern.h
create mode 100644 interfaces/kfc/rc.h
create mode 100644 interfaces/kfc/refcount-impl.h
create mode 100644 interfaces/kfc/refcount.h
create mode 100644 interfaces/kfc/rsrc-global.h
create mode 100644 interfaces/kfc/rsrc.h
create mode 100644 interfaces/kfc/tstate.h
create mode 100644 interfaces/kfc/vtbl-impl.h
create mode 100644 interfaces/kfc/xc.h
create mode 100644 interfaces/kfc/xcdefs.h
create mode 100644 interfaces/kfc/xcext.h
create mode 100644 interfaces/kfc/xcgen.h
create mode 100644 interfaces/kfg/config.h
create mode 100644 interfaces/kfg/extern.h
create mode 100644 interfaces/kfg/kart.h
create mode 100644 interfaces/kfg/keystore-priv.h
create mode 100644 interfaces/kfg/keystore.h
create mode 100644 interfaces/kfg/kfg-priv.h
create mode 100644 interfaces/kfg/ngc.h
create mode 100644 interfaces/kfg/properties.h
create mode 100644 interfaces/kfg/repository.h
create mode 100644 interfaces/kfs/arc.h
create mode 100644 interfaces/kfs/arrayfile.h
create mode 100644 interfaces/kfs/buffile.h
create mode 100644 interfaces/kfs/bzip.h
create mode 100644 interfaces/kfs/cacheteefile.h
create mode 100644 interfaces/kfs/countfile.h
create mode 100644 interfaces/kfs/crc.h
create mode 100644 interfaces/kfs/defs.h
create mode 100644 interfaces/kfs/directory.h
create mode 100644 interfaces/kfs/directory.hpp
create mode 100644 interfaces/kfs/dyload.h
create mode 100644 interfaces/kfs/extendable-ramfile.h
create mode 100644 interfaces/kfs/extern.h
create mode 100644 interfaces/kfs/ffext.h
create mode 100644 interfaces/kfs/ffmagic.h
create mode 100644 interfaces/kfs/file-impl.h
create mode 100644 interfaces/kfs/file-v1.h
create mode 100644 interfaces/kfs/file-v2.h
create mode 100644 interfaces/kfs/file.h
create mode 100644 interfaces/kfs/file.hpp
create mode 100644 interfaces/kfs/fileformat.h
create mode 100644 interfaces/kfs/filetools.h
create mode 100644 interfaces/kfs/gzip.h
create mode 100644 interfaces/kfs/impl.h
create mode 100644 interfaces/kfs/kfs-priv.h
create mode 100644 interfaces/kfs/lockfile.h
create mode 100644 interfaces/kfs/manager.h
create mode 100644 interfaces/kfs/md5.h
create mode 100644 interfaces/kfs/mmap.h
create mode 100644 interfaces/kfs/nullfile.h
create mode 100644 interfaces/kfs/pagefile.h
create mode 100644 interfaces/kfs/path-priv.h
create mode 100644 interfaces/kfs/path.h
create mode 100644 interfaces/kfs/pmem.h
create mode 100644 interfaces/kfs/quickmount.h
create mode 100644 interfaces/kfs/ramfile.h
create mode 100644 interfaces/kfs/readheadfile.h
create mode 100644 interfaces/kfs/sra.h
create mode 100644 interfaces/kfs/subfile.h
create mode 100644 interfaces/kfs/szip.h
create mode 100644 interfaces/kfs/tar.h
create mode 100644 interfaces/kfs/teefile.h
create mode 100644 interfaces/kfs/toc.h
create mode 100644 interfaces/kfs/wgaencrypt.h
create mode 100644 interfaces/klib/btree.h
create mode 100644 interfaces/klib/callconv.h
create mode 100644 interfaces/klib/checksum.h
create mode 100644 interfaces/klib/container.h
create mode 100644 interfaces/klib/data-buffer.h
create mode 100644 interfaces/klib/debug.h
create mode 100644 interfaces/klib/defs.h
create mode 100644 interfaces/klib/extern.h
create mode 100644 interfaces/klib/impl.h
create mode 100644 interfaces/klib/klib-priv.h
create mode 100644 interfaces/klib/ksort-macro.h
create mode 100644 interfaces/klib/log.h
create mode 100644 interfaces/klib/logfmt.h
create mode 100644 interfaces/klib/misc.h
create mode 100644 interfaces/klib/namelist.h
create mode 100644 interfaces/klib/namelist.hpp
create mode 100644 interfaces/klib/ncbi-vdb-version.h
create mode 100644 interfaces/klib/num-gen.h
create mode 100644 interfaces/klib/out.h
create mode 100644 interfaces/klib/pack.h
create mode 100644 interfaces/klib/path-priv.h
create mode 100644 interfaces/klib/path.h
create mode 100644 interfaces/klib/pbstree.h
create mode 100644 interfaces/klib/printf.h
create mode 100644 interfaces/klib/progressbar.h
create mode 100644 interfaces/klib/ptrie.h
create mode 100644 interfaces/klib/rc.h
create mode 100644 interfaces/klib/refcount.h
create mode 100644 interfaces/klib/report.h
create mode 100644 interfaces/klib/sort.h
create mode 100644 interfaces/klib/sra-release-version.h
create mode 100644 interfaces/klib/status.h
create mode 100644 interfaces/klib/symbol.h
create mode 100644 interfaces/klib/symtab.h
create mode 100644 interfaces/klib/text.h
create mode 100644 interfaces/klib/time.h
create mode 100644 interfaces/klib/token.h
create mode 100644 interfaces/klib/trie.h
create mode 100644 interfaces/klib/vector.h
create mode 100644 interfaces/klib/vlen-encode.h
create mode 100644 interfaces/klib/writer.h
create mode 100644 interfaces/kns/adapt.h
create mode 100644 interfaces/kns/ascp.h
create mode 100644 interfaces/kns/endpoint.h
create mode 100644 interfaces/kns/extern.h
create mode 100644 interfaces/kns/http-priv.h
create mode 100644 interfaces/kns/http.h
create mode 100644 interfaces/kns/impl.h
create mode 100644 interfaces/kns/kns-mgr-priv.h
create mode 100644 interfaces/kns/manager-ext.h
create mode 100644 interfaces/kns/manager.h
create mode 100644 interfaces/kns/socket.h
create mode 100644 interfaces/kns/stream.h
create mode 100644 interfaces/kns/tls.h
create mode 100644 interfaces/kproc/barrier.h
create mode 100644 interfaces/kproc/barrier.hpp
create mode 100644 interfaces/kproc/cond.h
create mode 100644 interfaces/kproc/cond.hpp
create mode 100644 interfaces/kproc/extern.h
create mode 100644 interfaces/kproc/impl.h
create mode 100644 interfaces/kproc/lock.h
create mode 100644 interfaces/kproc/lock.hpp
create mode 100644 interfaces/kproc/procmgr.h
create mode 100644 interfaces/kproc/q-extern.h
create mode 100644 interfaces/kproc/queue.h
create mode 100644 interfaces/kproc/sem.h
create mode 100644 interfaces/kproc/sem.hpp
create mode 100644 interfaces/kproc/task.h
create mode 100644 interfaces/kproc/thread.h
create mode 100644 interfaces/kproc/thread.hpp
create mode 100644 interfaces/kproc/timeout.h
create mode 100644 interfaces/krypto/aes-priv.h
create mode 100644 interfaces/krypto/cipher-impl.h
create mode 100644 interfaces/krypto/cipher-priv.h
create mode 100644 interfaces/krypto/cipher-test.h
create mode 100644 interfaces/krypto/cipher.h
create mode 100644 interfaces/krypto/ciphermgr-priv.h
create mode 100644 interfaces/krypto/ciphermgr.h
create mode 100644 interfaces/krypto/encfile-priv.h
create mode 100644 interfaces/krypto/encfile.h
create mode 100644 interfaces/krypto/extern.h
create mode 100644 interfaces/krypto/key.h
create mode 100644 interfaces/krypto/manager-priv.h
create mode 100644 interfaces/krypto/manager.h
create mode 100644 interfaces/krypto/reencfile.h
create mode 100644 interfaces/krypto/rng-impl.h
create mode 100644 interfaces/krypto/rng.h
create mode 100644 interfaces/krypto/testciphermgr.h
create mode 100644 interfaces/krypto/wgaencrypt.h
create mode 100644 interfaces/ktst/test_tools.hpp
create mode 100644 interfaces/ktst/unit_test.hpp
create mode 100644 interfaces/ktst/unit_test_suite.hpp
create mode 100644 interfaces/kxml/xml.h
create mode 100644 interfaces/kxml/xml.hpp
create mode 100644 interfaces/loader/alignment-writer.h
create mode 100644 interfaces/loader/common-reader-priv.h
create mode 100644 interfaces/loader/common-reader.h
create mode 100644 interfaces/loader/common-writer.h
create mode 100644 interfaces/loader/mmarray.h
create mode 100644 interfaces/loader/reference-writer.h
create mode 100644 interfaces/loader/sequence-writer.h
create mode 100644 interfaces/ncbi/clip.vschema
create mode 100644 interfaces/ncbi/extern.h
create mode 100644 interfaces/ncbi/kimpl-sra-cgi.h
create mode 100644 interfaces/ncbi/ksra-cgi-lib.h
create mode 100644 interfaces/ncbi/ksra-cgi.h
create mode 100644 interfaces/ncbi/ncbi.h
create mode 100644 interfaces/ncbi/ncbi.vschema
create mode 100644 interfaces/ncbi/pnbrdb.vschema
create mode 100644 interfaces/ncbi/seq-graph.vschema
create mode 100644 interfaces/ncbi/seq.vschema
create mode 100644 interfaces/ncbi/spotname.h
create mode 100644 interfaces/ncbi/spotname.vschema
create mode 100644 interfaces/ncbi/sra.vschema
create mode 100644 interfaces/ncbi/stats.vschema
create mode 100644 interfaces/ncbi/varloc.vschema
create mode 100644 interfaces/ncbi/vdb-blast-priv.h
create mode 100644 interfaces/ncbi/vdb-blast.h
create mode 100644 interfaces/ncbi/wgs-contig.h
create mode 100644 interfaces/ncbi/wgs-contig.vschema
create mode 100644 interfaces/ngs/Model.graphml
create mode 100644 interfaces/ngs/NOTES.txt
create mode 100644 interfaces/ngs/SimpleModel.graphml
create mode 100644 interfaces/ngs/cstdint
create mode 100644 interfaces/ngs/ncbi/NGS.hpp
create mode 100644 interfaces/os/linux/os-native.h
create mode 100644 interfaces/os/unix/oserror.h
create mode 100644 interfaces/os/unix/sysalloc.h
create mode 100644 interfaces/os/unix/unix-native.h
create mode 100644 interfaces/rdbms/rdbms.h
create mode 100644 interfaces/rdbms/sybase.h
create mode 100644 interfaces/search/extern.h
create mode 100644 interfaces/search/grep.h
create mode 100644 interfaces/search/nucstrstr.h
create mode 100644 interfaces/search/ref-variation.h
create mode 100644 interfaces/search/smith-waterman.h
create mode 100644 interfaces/simple/extern.h
create mode 100644 interfaces/simple/sra.hpp
create mode 100644 interfaces/sra/454.vschema
create mode 100644 interfaces/sra/abi.h
create mode 100644 interfaces/sra/abi.vschema
create mode 100644 interfaces/sra/extern.h
create mode 100644 interfaces/sra/fastq.h
create mode 100644 interfaces/sra/generic-fastq.vschema
create mode 100644 interfaces/sra/helicos.vschema
create mode 100644 interfaces/sra/illumina.h
create mode 100644 interfaces/sra/illumina.vschema
create mode 100644 interfaces/sra/impl.h
create mode 100644 interfaces/sra/ion-torrent.vschema
create mode 100644 interfaces/sra/nanopore.vschema
create mode 100644 interfaces/sra/pacbio.h
create mode 100644 interfaces/sra/pacbio.vschema
create mode 100644 interfaces/sra/path-extern.h
create mode 100644 interfaces/sra/pevents.vschema
create mode 100644 interfaces/sra/rd-extern.h
create mode 100644 interfaces/sra/sch-extern.h
create mode 100644 interfaces/sra/sff-file.h
create mode 100644 interfaces/sra/sff.h
create mode 100644 interfaces/sra/sradb-priv.h
create mode 100644 interfaces/sra/sradb.h
create mode 100644 interfaces/sra/sradb.hpp
create mode 100644 interfaces/sra/srapath.h
create mode 100644 interfaces/sra/srapath.hpp
create mode 100644 interfaces/sra/sraschema.h
create mode 100644 interfaces/sra/types.h
create mode 100644 interfaces/sra/wsradb.h
create mode 100644 interfaces/sra/wsradb.hpp
create mode 100644 interfaces/svdb/extern.h
create mode 100644 interfaces/svdb/svdb.h
create mode 100644 interfaces/tui/extern.h
create mode 100644 interfaces/tui/tui.h
create mode 100644 interfaces/tui/tui.hpp
create mode 100644 interfaces/tui/tui_dlg.h
create mode 100644 interfaces/vdb/blob.h
create mode 100644 interfaces/vdb/built-in.vschema
create mode 100644 interfaces/vdb/cursor.h
create mode 100644 interfaces/vdb/cursor.hpp
create mode 100644 interfaces/vdb/database.h
create mode 100644 interfaces/vdb/database.hpp
create mode 100644 interfaces/vdb/dependencies.h
create mode 100644 interfaces/vdb/extern.h
create mode 100644 interfaces/vdb/manager.h
create mode 100644 interfaces/vdb/manager.hpp
create mode 100644 interfaces/vdb/report.h
create mode 100644 interfaces/vdb/schema.h
create mode 100644 interfaces/vdb/schema.hpp
create mode 100644 interfaces/vdb/table.h
create mode 100644 interfaces/vdb/table.hpp
create mode 100644 interfaces/vdb/types.h
create mode 100644 interfaces/vdb/types.hpp
create mode 100644 interfaces/vdb/vdb-priv.h
create mode 100644 interfaces/vdb/vdb.h
create mode 100644 interfaces/vdb/vdb.vschema
create mode 100644 interfaces/vdb/xform.h
create mode 100644 interfaces/vfs/extern.h
create mode 100644 interfaces/vfs/keyring-priv.h
create mode 100644 interfaces/vfs/manager-priv.h
create mode 100644 interfaces/vfs/manager.h
create mode 100644 interfaces/vfs/path-priv.h
create mode 100644 interfaces/vfs/path.h
create mode 100644 interfaces/vfs/resolver.h
create mode 100644 interfaces/xfs/doc.h
create mode 100644 interfaces/xfs/editors.h
create mode 100644 interfaces/xfs/extern.h
create mode 100644 interfaces/xfs/handle.h
create mode 100644 interfaces/xfs/model.h
create mode 100644 interfaces/xfs/node.h
create mode 100644 interfaces/xfs/path.h
create mode 100644 interfaces/xfs/perm.h
create mode 100644 interfaces/xfs/tree.h
create mode 100644 interfaces/xfs/xfs-defs.h
create mode 100644 interfaces/xfs/xfs.h
create mode 100644 interfaces/xfs/xlog.h
create mode 100644 libs/Makefile
create mode 100644 libs/align/.gitignore
create mode 100644 libs/align/Makefile
create mode 100644 libs/align/al_iterator.c
create mode 100644 libs/align/align-access.c
create mode 100644 libs/align/align_mgr.c
create mode 100644 libs/align/bam-priv.h
create mode 100644 libs/align/bam.c
create mode 100644 libs/align/debug.h
create mode 100644 libs/align/dna-reverse-cmpl.c
create mode 100644 libs/align/pl_iterator.c
create mode 100644 libs/align/quality-quantizer.c
create mode 100644 libs/align/reader-cmn.c
create mode 100644 libs/align/reader-cmn.h
create mode 100644 libs/align/reader-refseq.c
create mode 100644 libs/align/reader-wgs.c
create mode 100644 libs/align/reader-wgs.h
create mode 100644 libs/align/ref_iterator.c
create mode 100644 libs/align/reference-cmn.c
create mode 100644 libs/align/reference-cmn.h
create mode 100644 libs/align/reference.c
create mode 100644 libs/align/refseq-mgr-priv.h
create mode 100644 libs/align/refseq-mgr.c
create mode 100644 libs/align/writer-alignment.c
create mode 100644 libs/align/writer-cmn.c
create mode 100644 libs/align/writer-priv.h
create mode 100644 libs/align/writer-ref.c
create mode 100644 libs/align/writer-ref.h
create mode 100644 libs/align/writer-reference.c
create mode 100644 libs/align/writer-refseq.c
create mode 100644 libs/align/writer-sequence.c
create mode 100644 libs/ascp/Makefile
create mode 100644 libs/ascp/ascp-priv.h
create mode 100644 libs/ascp/ascp.c
create mode 100644 libs/ascp/linux/ascp-path.c
create mode 100644 libs/ascp/unix/connect.c
create mode 100644 libs/axf/.gitignore
create mode 100644 libs/axf/Makefile
create mode 100644 libs/axf/align-local_ref_id.c
create mode 100644 libs/axf/align-local_ref_start.c
create mode 100644 libs/axf/align-ref-name.c
create mode 100644 libs/axf/align-ref-pos.c
create mode 100644 libs/axf/align-ref-seq-id.c
create mode 100644 libs/axf/align-restore-read.c
create mode 100644 libs/axf/cigar.c
create mode 100644 libs/axf/generate-mismatch-qual.c
create mode 100644 libs/axf/get-sam-flags.c
create mode 100644 libs/axf/get_mate_align_ids.c
create mode 100644 libs/axf/make-cmp-read_desc.c
create mode 100644 libs/axf/mismatch-restore-qual.c
create mode 100644 libs/axf/not-my-row.c
create mode 100644 libs/axf/project_read_from_sequence.c
create mode 100644 libs/axf/raw-restore-qual.c
create mode 100644 libs/axf/raw-restore-read.c
create mode 100644 libs/axf/ref-preserve_qual.c
create mode 100644 libs/axf/ref-restore-read.c
create mode 100644 libs/axf/ref-tbl-sub-select.c
create mode 100644 libs/axf/ref-tbl.c
create mode 100644 libs/axf/ref-tbl.h
create mode 100644 libs/axf/refseq-stats.c
create mode 100644 libs/axf/seq-construct-read.c
create mode 100644 libs/axf/seq-restore-linkage-group.c
create mode 100644 libs/axf/seq-restore-read.c
create mode 100644 libs/axf/template-len.c
create mode 100644 libs/blast/Makefile
create mode 100644 libs/blast/blast-mgr.c
create mode 100644 libs/blast/blast-mgr.h
create mode 100644 libs/blast/reader.c
create mode 100644 libs/blast/reader.h
create mode 100644 libs/blast/reference.c
create mode 100644 libs/blast/reference.h
create mode 100644 libs/blast/run-set.c
create mode 100644 libs/blast/run-set.h
create mode 100644 libs/cipher/cipher-1.7/PKG-INFO
create mode 100644 libs/cipher/cipher-1.7/README.md
create mode 100644 libs/cipher/cipher-1.7/cipher.egg-info/PKG-INFO
create mode 100644 libs/cipher/cipher-1.7/cipher.egg-info/SOURCES.txt
create mode 100644 libs/cipher/cipher-1.7/cipher.egg-info/dependency_links.txt
create mode 100644 libs/cipher/cipher-1.7/cipher.egg-info/not-zip-safe
create mode 100644 libs/cipher/cipher-1.7/cipher.egg-info/top_level.txt
create mode 100644 libs/cipher/cipher-1.7/cipher/__init__.py
create mode 100644 libs/cipher/cipher-1.7/decrypt.py
create mode 100644 libs/cipher/cipher-1.7/encrypt.py
create mode 100644 libs/cipher/cipher-1.7/requirements-test.txt
create mode 100644 libs/cipher/cipher-1.7/setup.cfg
create mode 100644 libs/cipher/cipher-1.7/setup.py
create mode 100644 libs/csra2/Makefile
create mode 100644 libs/hdf5/.gitignore
create mode 100644 libs/hdf5/Makefile
create mode 100644 libs/hdf5/hdf5arrayfile-priv.h
create mode 100644 libs/hdf5/hdf5arrayfile.c
create mode 100644 libs/hdf5/hdf5dir.c
create mode 100644 libs/hdf5/hdf5file.c
create mode 100644 libs/kapp/Makefile
create mode 100644 libs/kapp/args-conv.c
create mode 100644 libs/kapp/args.c
create mode 100644 libs/kapp/args_debug.h
create mode 100644 libs/kapp/linux/ram.c
create mode 100644 libs/kapp/loader-file.c
create mode 100644 libs/kapp/loader-meta.c
create mode 100644 libs/kapp/log-xml.c
create mode 100644 libs/kapp/main-priv.h
create mode 100644 libs/kapp/main.c
create mode 100644 libs/kapp/progressbar.c
create mode 100644 libs/kapp/queue-file.c
create mode 100644 libs/kapp/tokenizer.c
create mode 100644 libs/kapp/unix/args-conv-os.c
create mode 100644 libs/kapp/unix/sysmain.c
rename {src/test/java/htsjdk/samtools/apps => libs/kdb}/.gitignore (100%)
create mode 100644 libs/kdb/Makefile
create mode 100644 libs/kdb/btree.c
create mode 100644 libs/kdb/cc-priv.h
create mode 100644 libs/kdb/coldata-priv.h
create mode 100644 libs/kdb/coldata.c
create mode 100644 libs/kdb/colfmt-priv.h
create mode 100644 libs/kdb/colidx-priv.h
create mode 100644 libs/kdb/colidx.c
create mode 100644 libs/kdb/colidx0-priv.h
create mode 100644 libs/kdb/colidx0.c
create mode 100644 libs/kdb/colidx1-priv.h
create mode 100644 libs/kdb/colidx1.c
create mode 100644 libs/kdb/colidx2-priv.h
create mode 100644 libs/kdb/colidx2.c
create mode 100644 libs/kdb/column-cc.c
create mode 100644 libs/kdb/column-priv.h
create mode 100644 libs/kdb/column.c
create mode 100644 libs/kdb/database-cc.c
create mode 100644 libs/kdb/database-cmn.c
create mode 100644 libs/kdb/database-priv.h
create mode 100644 libs/kdb/database.c
create mode 100644 libs/kdb/dbcc-cmn.c
create mode 100644 libs/kdb/dbmgr-cmn.c
create mode 100644 libs/kdb/dbmgr-priv.h
create mode 100644 libs/kdb/dbmgr.c
create mode 100644 libs/kdb/idstats-priv.h
create mode 100644 libs/kdb/idstats.c
create mode 100644 libs/kdb/idxblk-priv.h
create mode 100644 libs/kdb/idxblk.c
create mode 100644 libs/kdb/index-cmn.h
create mode 100644 libs/kdb/index-priv.h
create mode 100644 libs/kdb/index.c
create mode 100644 libs/kdb/kdb-priv.h
create mode 100644 libs/kdb/kdb.c
create mode 100644 libs/kdb/kdbfmt-priv.h
create mode 100644 libs/kdb/libkdb.vers.h
create mode 100644 libs/kdb/meta.c
create mode 100644 libs/kdb/ptrieval-v1.c
create mode 100644 libs/kdb/ptrieval-v2.c
create mode 100644 libs/kdb/rowset-it.c_old
create mode 100644 libs/kdb/rowset-priv.h_old
create mode 100644 libs/kdb/rowset-simple.c
create mode 100644 libs/kdb/rowset.c
create mode 100644 libs/kdb/rowset.c_old
create mode 100644 libs/kdb/table-cc.c
create mode 100644 libs/kdb/table-priv.h
create mode 100644 libs/kdb/table.c
create mode 100644 libs/kdb/trieidx-priv.h
create mode 100644 libs/kdb/trieidx-v1.c
create mode 100644 libs/kdb/trieidx-v2.c
create mode 100644 libs/kdb/trieval-v1.c
create mode 100644 libs/kdb/trieval-v2.c
create mode 100644 libs/kdb/u64idx-v3.c
create mode 100644 libs/kdb/wcoldata-priv.h
create mode 100644 libs/kdb/wcoldata.c
create mode 100644 libs/kdb/wcolidx-priv.h
create mode 100644 libs/kdb/wcolidx.c
create mode 100644 libs/kdb/wcolidx0-priv.h
create mode 100644 libs/kdb/wcolidx0.c
create mode 100644 libs/kdb/wcolidx1-priv.h
create mode 100644 libs/kdb/wcolidx1.c
create mode 100644 libs/kdb/wcolidx2-priv.h
create mode 100644 libs/kdb/wcolidx2.c
create mode 100644 libs/kdb/wcolumn-priv.h
create mode 100644 libs/kdb/wcolumn.c
create mode 100644 libs/kdb/wdatabase-priv.h
create mode 100644 libs/kdb/wdatabase.c
create mode 100644 libs/kdb/wdbmgr.c
create mode 100644 libs/kdb/werror-priv.h
create mode 100644 libs/kdb/widxblk-priv.h
create mode 100644 libs/kdb/widxblk.c
create mode 100644 libs/kdb/windex-priv.h
create mode 100644 libs/kdb/windex.c
create mode 100644 libs/kdb/wkdb-priv.h
create mode 100644 libs/kdb/wkdb.c
create mode 100644 libs/kdb/wmeta.c
create mode 100644 libs/kdb/wtable-priv.h
create mode 100644 libs/kdb/wtable.c
create mode 100644 libs/kdb/wtrieidx-v1.c
create mode 100644 libs/kdb/wtrieidx-v2.c
create mode 100644 libs/kdb/wu64idx-v3.c
create mode 100644 libs/kfc/Makefile
create mode 100644 libs/kfc/except.c
create mode 100644 libs/kfc/refcount.c
create mode 100644 libs/kfc/rsrc-priv.h
create mode 100644 libs/kfc/rsrc.c
create mode 100644 libs/kfc/sysctx-priv.h
create mode 100644 libs/kfc/tstate.c
create mode 100644 libs/kfc/unix/sysctx.c
create mode 100644 libs/kfc/unix/sysrsrc.c
create mode 100644 libs/kfc/vtbl.c
create mode 100644 libs/kfc/xc.c
create mode 100644 libs/kfg/.gitignore
create mode 100644 libs/kfg/Makefile
create mode 100644 libs/kfg/certs.kfg
create mode 100644 libs/kfg/config-aws.c
create mode 100644 libs/kfg/config-grammar.c
create mode 100644 libs/kfg/config-grammar.y
create mode 100644 libs/kfg/config-lex.c
create mode 100644 libs/kfg/config-lex.l
create mode 100644 libs/kfg/config-tokens.h
create mode 100644 libs/kfg/config.c
create mode 100644 libs/kfg/default.kfg
create mode 100644 libs/kfg/kart.c
create mode 100644 libs/kfg/keystore.c
create mode 100644 libs/kfg/kfg-lex.h
create mode 100644 libs/kfg/kfg-parse.h
create mode 100644 libs/kfg/kfg-priv.h
create mode 100644 libs/kfg/ngc-priv.h
create mode 100644 libs/kfg/ngc.c
create mode 100644 libs/kfg/properties.c
create mode 100644 libs/kfg/report-kfg.c
create mode 100644 libs/kfg/repository.c
create mode 100644 libs/kfs/.gitignore
create mode 100644 libs/kfs/Makefile
create mode 100644 libs/kfs/arc.c
create mode 100644 libs/kfs/arrayfile.c
create mode 100644 libs/kfs/buffile-read.c
create mode 100644 libs/kfs/buffile-write.c
create mode 100644 libs/kfs/buffile.c
create mode 100644 libs/kfs/bzip.c
create mode 100644 libs/kfs/cacheteefile.c
create mode 100644 libs/kfs/countfile.c
create mode 100644 libs/kfs/crc32.c
create mode 100644 libs/kfs/dir_test.c
create mode 100644 libs/kfs/directory-v2.c
create mode 100644 libs/kfs/directory.c
create mode 100644 libs/kfs/extendable-ramfile.c
create mode 100644 libs/kfs/ffext.c
create mode 100644 libs/kfs/ffkey.c
create mode 100644 libs/kfs/ffmagic.c
create mode 100644 libs/kfs/file-v2.c
create mode 100644 libs/kfs/file.c
create mode 100644 libs/kfs/fileformat-priv.h
create mode 100644 libs/kfs/fileformat.c
create mode 100644 libs/kfs/from_to_namelist.c
create mode 100644 libs/kfs/gzip.c
create mode 100644 libs/kfs/impl.h
create mode 100644 libs/kfs/karc-priv.h
create mode 100644 libs/kfs/kfs-priv.h
create mode 100644 libs/kfs/kfsmagic
create mode 100644 libs/kfs/lockfile.c
create mode 100644 libs/kfs/manager.c
create mode 100644 libs/kfs/md5.c
create mode 100644 libs/kfs/mmap-priv.h
create mode 100644 libs/kfs/mmap.c
create mode 100644 libs/kfs/nullfile.c
create mode 100644 libs/kfs/pagefile.c
create mode 100644 libs/kfs/pmem.c
create mode 100644 libs/kfs/quickmount.c
create mode 100644 libs/kfs/ramfile.c
create mode 100644 libs/kfs/readheadfile.c
create mode 100644 libs/kfs/report.c
create mode 100644 libs/kfs/sra.c
create mode 100644 libs/kfs/subfile.c
create mode 100644 libs/kfs/szip.c
create mode 100644 libs/kfs/tar.c
create mode 100644 libs/kfs/teefile.c
create mode 100644 libs/kfs/toc-priv.h
create mode 100644 libs/kfs/toc.c
create mode 100644 libs/kfs/tocdir.c
create mode 100644 libs/kfs/tocentry.c
create mode 100644 libs/kfs/tocfile.c
create mode 100644 libs/kfs/unix/sysdir-priv.h
create mode 100644 libs/kfs/unix/sysdir.c
create mode 100644 libs/kfs/unix/sysdll.c
create mode 100644 libs/kfs/unix/sysfile-priv.h
create mode 100644 libs/kfs/unix/sysfile-v2.c
create mode 100644 libs/kfs/unix/sysfile.c
create mode 100644 libs/kfs/unix/syslockfile.c
create mode 100644 libs/kfs/unix/sysmmap-priv.h
create mode 100644 libs/kfs/unix/sysmmap.c
create mode 100644 libs/klib/.gitignore
create mode 100644 libs/klib/Judy.h
create mode 100644 libs/klib/Makefile
create mode 100644 libs/klib/SHA-32bit.c
create mode 100644 libs/klib/SHA-64bit.c
create mode 100644 libs/klib/bsd/syserrcode.c
create mode 100644 libs/klib/bsearch.c
create mode 100644 libs/klib/bstpersist.c
create mode 100644 libs/klib/btree.c
create mode 100644 libs/klib/container.c
create mode 100644 libs/klib/cp1252.c
create mode 100644 libs/klib/crc32.c
create mode 100644 libs/klib/data-buffer.c
create mode 100644 libs/klib/debug.c
create mode 100644 libs/klib/iso8859-1.c
create mode 100644 libs/klib/iso8859.c
create mode 100644 libs/klib/judy-vector.c
rename {src/test/java/htsjdk/samtools/fastq => libs/klib/judy}/.gitignore (100%)
create mode 100644 libs/klib/judy/Judy1.h
create mode 100644 libs/klib/judy/Judy1Tables.32.c
create mode 100644 libs/klib/judy/Judy1Tables.64.c
create mode 100644 libs/klib/judy/JudyByCount.c
create mode 100644 libs/klib/judy/JudyByCountWithDefs.c
create mode 100644 libs/klib/judy/JudyCascade.c
create mode 100644 libs/klib/judy/JudyCount.c
create mode 100644 libs/klib/judy/JudyCreateBranch.c
create mode 100644 libs/klib/judy/JudyDecascade.c
create mode 100644 libs/klib/judy/JudyDel.c
create mode 100644 libs/klib/judy/JudyFirst.c
create mode 100644 libs/klib/judy/JudyFreeArray.c
create mode 100644 libs/klib/judy/JudyGet.c
create mode 100644 libs/klib/judy/JudyHS.c
create mode 100644 libs/klib/judy/JudyHS.h
create mode 100644 libs/klib/judy/JudyIns.c
create mode 100644 libs/klib/judy/JudyInsArray.c
create mode 100644 libs/klib/judy/JudyInsertBranch.c
create mode 100644 libs/klib/judy/JudyL.h
create mode 100644 libs/klib/judy/JudyLTables.32.c
create mode 100644 libs/klib/judy/JudyLTables.64.c
create mode 100644 libs/klib/judy/JudyMalloc.c
create mode 100644 libs/klib/judy/JudyMallocIF.c
create mode 100644 libs/klib/judy/JudyMemActive.c
create mode 100644 libs/klib/judy/JudyMemUsed.c
create mode 100644 libs/klib/judy/JudyNext.c
create mode 100644 libs/klib/judy/JudyNextEmpty.c
create mode 100644 libs/klib/judy/JudyPrev.c
create mode 100644 libs/klib/judy/JudyPrevEmpty.c
create mode 100644 libs/klib/judy/JudyPrevNext.c
create mode 100644 libs/klib/judy/JudyPrevNextEmpty.c
create mode 100644 libs/klib/judy/JudyPrintJP.c
create mode 100644 libs/klib/judy/JudyPrivate.h
create mode 100644 libs/klib/judy/JudyPrivate1L.h
create mode 100644 libs/klib/judy/JudyPrivateBranch.h
create mode 100644 libs/klib/judy/JudySL.c
create mode 100644 libs/klib/judy/JudyTablesGen.c
create mode 100644 libs/klib/judy/Judy_Bit.c
create mode 100644 libs/klib/judy/Judy_Bit_Cascade.c
create mode 100644 libs/klib/judy/Judy_Bit_Count.c
create mode 100644 libs/klib/judy/Judy_Bit_Decascade.c
create mode 100644 libs/klib/judy/Judy_Bit_Next.c
create mode 100644 libs/klib/judy/Judy_Bit_NextEmpty.c
create mode 100644 libs/klib/judy/Judy_Bit_Prev.c
create mode 100644 libs/klib/judy/Judy_Word.c
create mode 100644 libs/klib/judy/Judy_Word_Cascade.c
create mode 100644 libs/klib/judy/Judy_Word_Count.c
create mode 100644 libs/klib/judy/Judy_Word_Decascade.c
create mode 100644 libs/klib/judy/Judy_Word_Next.c
create mode 100644 libs/klib/judy/Judy_Word_NextEmpty.c
create mode 100644 libs/klib/judy/Judy_Word_Prev.c
create mode 100644 libs/klib/judy/Makefile
create mode 100644 libs/klib/judy/_Judy1Tables.c
create mode 100644 libs/klib/judy/_JudyLTables.c
create mode 100644 libs/klib/judy/j__udyGet.c
create mode 100644 libs/klib/ksort.c
create mode 100644 libs/klib/linux/syserrcode.c
create mode 100644 libs/klib/log-priv.h
create mode 100644 libs/klib/log.c
create mode 100644 libs/klib/maybeswap.h
create mode 100644 libs/klib/md5.c
create mode 100644 libs/klib/namelist.c
create mode 100644 libs/klib/ncbi-vdb-version.c
create mode 100644 libs/klib/num-gen.c
create mode 100644 libs/klib/out.c
create mode 100644 libs/klib/pack.c
create mode 100644 libs/klib/pbstree-impl.c
create mode 100644 libs/klib/pbstree-native.c
create mode 100644 libs/klib/pbstree-priv.h
create mode 100644 libs/klib/pbstree-swapped.c
create mode 100644 libs/klib/pbstree.c
create mode 100644 libs/klib/printf.c
create mode 100644 libs/klib/progressbar.c
create mode 100644 libs/klib/ptpersist.c
create mode 100644 libs/klib/ptrie.c
create mode 100644 libs/klib/qsort.c
create mode 100644 libs/klib/rc-idx-tbl.c
create mode 100644 libs/klib/rc-tbl.c
create mode 100644 libs/klib/refcount.c
create mode 100644 libs/klib/release-vers.h
create mode 100644 libs/klib/report-klib.c
create mode 100644 libs/klib/sra-release-version.c
create mode 100644 libs/klib/status-rc-strings.c
create mode 100644 libs/klib/status-rc.c
create mode 100644 libs/klib/status.c
create mode 100644 libs/klib/symtab.c
create mode 100644 libs/klib/text.c
create mode 100644 libs/klib/time.c
create mode 100644 libs/klib/token.c
create mode 100644 libs/klib/trie-priv.h
create mode 100644 libs/klib/trie.c
create mode 100644 libs/klib/trieval.c
create mode 100644 libs/klib/unix/misc.c
create mode 100644 libs/klib/unix/syserrcode.c
create mode 100644 libs/klib/unix/syslog.c
create mode 100644 libs/klib/unix/systime.c
create mode 100644 libs/klib/unix/syswriter.c
create mode 100644 libs/klib/unpack.c
create mode 100644 libs/klib/utf8.c
create mode 100644 libs/klib/vector.c
create mode 100644 libs/klib/vector_namelist.c
create mode 100644 libs/klib/vlen-encode.c
create mode 100644 libs/klib/writer-priv.h
create mode 100644 libs/klib/writer.c
create mode 100644 libs/kns/Makefile
create mode 100644 libs/kns/buffered-stream.c
create mode 100644 libs/kns/endpoint.c
create mode 100644 libs/kns/http-client.c
create mode 100644 libs/kns/http-file.c
create mode 100644 libs/kns/http-priv.h
create mode 100644 libs/kns/http-retrier.c
create mode 100644 libs/kns/http.c
create mode 100644 libs/kns/kns_manager-ext.c
create mode 100644 libs/kns/kns_manager.c
create mode 100644 libs/kns/linux/sysendpoint.c
create mode 100644 libs/kns/linux/syspoll.c
create mode 100644 libs/kns/manager.c
create mode 100644 libs/kns/mgr-priv.h
create mode 100644 libs/kns/poll-priv.h
create mode 100644 libs/kns/stream-from-files.c
create mode 100644 libs/kns/stream-from-streams.c
create mode 100644 libs/kns/stream-priv.h
create mode 100644 libs/kns/stream.c
create mode 100644 libs/kns/sysmgr.h
create mode 100644 libs/kns/tls-priv.h
create mode 100644 libs/kns/tls.c
create mode 100644 libs/kns/unix/sysmgr.c
create mode 100644 libs/kns/unix/syssock.c
create mode 100644 libs/kns/unix/sysstream.c
create mode 100644 libs/kns/url-fetcher-curl.c
create mode 100644 libs/kns/url-fetcher-impl.h
create mode 100644 libs/kns/url-fetcher.c
create mode 100644 libs/kproc/Makefile
create mode 100644 libs/kproc/bsd/syslock-priv.h
create mode 100644 libs/kproc/bsd/syslock.c
create mode 100644 libs/kproc/bsd/sysmgr.c
create mode 100644 libs/kproc/linux/sysbarrier.c
create mode 100644 libs/kproc/linux/syslock-priv.h
create mode 100644 libs/kproc/linux/syslock.c
create mode 100644 libs/kproc/linux/sysmgr.c
create mode 100644 libs/kproc/procmgr.c
create mode 100644 libs/kproc/queue.c
create mode 100644 libs/kproc/sem.c
create mode 100644 libs/kproc/stbarrier.c
create mode 100644 libs/kproc/stcond.c
create mode 100644 libs/kproc/stlock.c
create mode 100644 libs/kproc/stsem.c
create mode 100644 libs/kproc/stthread.c
create mode 100644 libs/kproc/sttimeout.c
create mode 100644 libs/kproc/task.c
create mode 100644 libs/kproc/unix/syscond-priv.h
create mode 100644 libs/kproc/unix/syscond.c
create mode 100644 libs/kproc/unix/systhread.c
create mode 100644 libs/kproc/unix/systimeout.c
create mode 100644 libs/krypto/.gitignore
create mode 100644 libs/krypto/Makefile
create mode 100644 libs/krypto/aes-byte.c
create mode 100644 libs/krypto/aes-impl.c
create mode 100644 libs/krypto/aes-ncbi-ni.c
create mode 100644 libs/krypto/aes-ncbi-priv.h
create mode 100644 libs/krypto/aes-ncbi.c
create mode 100644 libs/krypto/aes-priv.h
create mode 100644 libs/krypto/aes.c
create mode 100644 libs/krypto/aes_core.c
create mode 100644 libs/krypto/aes_x86core.c
create mode 100644 libs/krypto/aesx86.c
create mode 100644 libs/krypto/blockcipher-byte-impl.h
create mode 100644 libs/krypto/blockcipher-impl.h
create mode 100644 libs/krypto/blockcipher-priv.h
create mode 100644 libs/krypto/blockcipher-vec-impl.h
create mode 100644 libs/krypto/blockcipher.c
create mode 100644 libs/krypto/cipher-byte.c
create mode 100644 libs/krypto/cipher-impl.h
create mode 100644 libs/krypto/cipher-no-vec.c
create mode 100644 libs/krypto/cipher-priv.h
create mode 100644 libs/krypto/cipher-vec.c
create mode 100644 libs/krypto/cipher.c
create mode 100644 libs/krypto/ciphermgr.c
create mode 100644 libs/krypto/ciphertest.c
create mode 100644 libs/krypto/compile-test.c
create mode 100644 libs/krypto/csprng.c
create mode 100644 libs/krypto/encfile-priv.h
create mode 100644 libs/krypto/encfile.c
create mode 100644 libs/krypto/encfilev2.c
create mode 100644 libs/krypto/key.c
create mode 100644 libs/krypto/manager.c
create mode 100644 libs/krypto/ncbi-priv.h
create mode 100644 libs/krypto/no-null-ncbi.c
create mode 100644 libs/krypto/null-ncbi-priv.h
create mode 100644 libs/krypto/null-ncbi.c
create mode 100644 libs/krypto/reencfile.c
create mode 100644 libs/krypto/rng-impl.h
rename src/test/java/htsjdk/tribble/source/.gitignore => libs/krypto/rng-priv.h (100%)
create mode 100644 libs/krypto/rng.c
create mode 100644 libs/krypto/testcipher.c
create mode 100644 libs/krypto/unix/sysrng.c
create mode 100644 libs/krypto/wgaencrypt.c
create mode 100644 libs/ktst/Makefile
create mode 100644 libs/ktst/testcase.cpp
create mode 100644 libs/ktst/testenv.cpp
create mode 100644 libs/ktst/testrunner.cpp
create mode 100644 libs/ktst/unix/systestenv.cpp
create mode 100644 libs/kxml/Makefile
create mode 100644 libs/kxml/xml.c
create mode 100644 libs/kxml/xtoc-parsexml.c
create mode 100644 libs/kxml/xtoc-priv.h
create mode 100644 libs/kxml/xtoc.c
create mode 100644 libs/loader/Makefile
create mode 100644 libs/loader/alignment-writer.c
create mode 100644 libs/loader/common-reader.c
create mode 100644 libs/loader/common-writer.c
create mode 100644 libs/loader/mmarray.c
create mode 100644 libs/loader/reference-writer.c
create mode 100644 libs/loader/sequence-writer.c
create mode 100644 libs/ncbi-vdb/Makefile
create mode 100644 libs/ncbi-vdb/libncbi-vdb.vers
create mode 100644 libs/ngs-c++/Makefile
create mode 100644 libs/ngs-c++/NCBI-NGS.cpp
create mode 100644 libs/ngs-c++/testy-the-bear.cpp
create mode 100644 libs/ngs-jni/.gitignore
create mode 100644 libs/ngs-jni/Makefile
create mode 100644 libs/ngs-jni/jni_ErrorMsg.c
create mode 100644 libs/ngs-jni/jni_ErrorMsg.h
create mode 100644 libs/ngs-jni/jni_Manager.c
create mode 100644 libs/ngs-jni/jni_Manager.h
create mode 100644 libs/ngs-jni/jni_String.c
create mode 100644 libs/ngs-jni/jni_String.h
create mode 100644 libs/ngs-py/Makefile
create mode 100644 libs/ngs-py/py_Manager.c
create mode 100644 libs/ngs-py/py_Manager.h
create mode 100644 libs/ngs-py/py_ngs_defs.h
create mode 100644 libs/ngs/BAM_Alignment.c
create mode 100644 libs/ngs/BAM_Alignment.h
create mode 100644 libs/ngs/BAM_ReadCollection.c
create mode 100644 libs/ngs/BAM_Record.c
create mode 100644 libs/ngs/BAM_Record.h
create mode 100644 libs/ngs/CSRA1_Alignment.c
create mode 100644 libs/ngs/CSRA1_Alignment.h
create mode 100644 libs/ngs/CSRA1_Pileup.c
create mode 100644 libs/ngs/CSRA1_Pileup.h
create mode 100644 libs/ngs/CSRA1_PileupEvent.c
create mode 100644 libs/ngs/CSRA1_PileupEvent.h
create mode 100644 libs/ngs/CSRA1_Read.c
create mode 100644 libs/ngs/CSRA1_Read.h
create mode 100644 libs/ngs/CSRA1_ReadCollection.c
create mode 100644 libs/ngs/CSRA1_ReadCollection.h
create mode 100644 libs/ngs/CSRA1_Reference.c
create mode 100644 libs/ngs/CSRA1_Reference.h
create mode 100644 libs/ngs/CSRA1_ReferenceWindow.c
create mode 100644 libs/ngs/CSRA1_ReferenceWindow.h
create mode 100644 libs/ngs/EBI_ReferenceSequence.c
create mode 100644 libs/ngs/EBI_ReferenceSequence.h
create mode 100644 libs/ngs/Makefile
create mode 100644 libs/ngs/Model.graphml
create mode 100644 libs/ngs/NCBI-NGS.c
create mode 100644 libs/ngs/NCBI-NGS.h
create mode 100644 libs/ngs/NGS_Alignment.c
create mode 100644 libs/ngs/NGS_Alignment.h
create mode 100644 libs/ngs/NGS_Cursor.c
create mode 100644 libs/ngs/NGS_Cursor.h
create mode 100644 libs/ngs/NGS_ErrBlock.c
create mode 100644 libs/ngs/NGS_ErrBlock.h
create mode 100644 libs/ngs/NGS_Fragment.c
create mode 100644 libs/ngs/NGS_Fragment.h
create mode 100644 libs/ngs/NGS_FragmentBlob.c
create mode 100644 libs/ngs/NGS_FragmentBlob.h
create mode 100644 libs/ngs/NGS_FragmentBlobIterator.c
create mode 100644 libs/ngs/NGS_FragmentBlobIterator.h
create mode 100644 libs/ngs/NGS_Id.c
create mode 100644 libs/ngs/NGS_Id.h
create mode 100644 libs/ngs/NGS_Pileup.c
create mode 100644 libs/ngs/NGS_Pileup.h
create mode 100644 libs/ngs/NGS_PileupEvent.c
create mode 100644 libs/ngs/NGS_PileupEvent.h
create mode 100644 libs/ngs/NGS_Read.c
create mode 100644 libs/ngs/NGS_Read.h
create mode 100644 libs/ngs/NGS_ReadCollection.c
create mode 100644 libs/ngs/NGS_ReadCollection.h
create mode 100644 libs/ngs/NGS_ReadGroup.c
create mode 100644 libs/ngs/NGS_ReadGroup.h
create mode 100644 libs/ngs/NGS_Refcount.c
create mode 100644 libs/ngs/NGS_Refcount.h
create mode 100644 libs/ngs/NGS_Reference.c
create mode 100644 libs/ngs/NGS_Reference.h
create mode 100644 libs/ngs/NGS_ReferenceSequence.c
create mode 100644 libs/ngs/NGS_ReferenceSequence.h
create mode 100644 libs/ngs/NGS_Statistics.c
create mode 100644 libs/ngs/NGS_Statistics.h
create mode 100644 libs/ngs/NGS_String.c
create mode 100644 libs/ngs/NGS_String.h
create mode 100644 libs/ngs/NOTES.txt
create mode 100644 libs/ngs/SRA_DB_ReadCollection.c
create mode 100644 libs/ngs/SRA_Read.c
create mode 100644 libs/ngs/SRA_Read.h
create mode 100644 libs/ngs/SRA_ReadCollection.c
create mode 100644 libs/ngs/SRA_ReadGroup.c
create mode 100644 libs/ngs/SRA_ReadGroup.h
create mode 100644 libs/ngs/SRA_ReadGroupInfo.c
create mode 100644 libs/ngs/SRA_ReadGroupInfo.h
create mode 100644 libs/ngs/SRA_ReferenceSequence.c
create mode 100644 libs/ngs/SRA_ReferenceSequence.h
create mode 100644 libs/ngs/SRA_Statistics.c
create mode 100644 libs/ngs/SRA_Statistics.h
create mode 100644 libs/ngs/VByteBlob.c
create mode 100644 libs/ngs/VByteBlob.h
create mode 100644 libs/ngs/extern.h
rename {src/test/resources/htsjdk/tribble/tmp => libs/search}/.gitignore (100%)
create mode 100644 libs/search/Makefile
create mode 100644 libs/search/agrep-dp.c
create mode 100644 libs/search/agrep-myers.c
create mode 100644 libs/search/agrep-myersunltd.c
create mode 100644 libs/search/agrep-wumanber.c
create mode 100644 libs/search/debug.h
create mode 100644 libs/search/fgrep-aho.c
create mode 100644 libs/search/fgrep-boyermoore.c
create mode 100644 libs/search/fgrep-dumb.c
create mode 100644 libs/search/nucstrstr.c
create mode 100644 libs/search/search-priv.h
create mode 100644 libs/search/search.c
create mode 100644 libs/search/sw-search.c
create mode 100644 libs/sra/.gitignore
create mode 100644 libs/sra/Makefile
create mode 100644 libs/sra/built-in.vschema
create mode 100644 libs/sra/libsra-schema.vers.h
create mode 100644 libs/sra/libsradb.vers.h
create mode 100644 libs/sra/libsrareader.vers.h
create mode 100644 libs/sra/libsraschema.vers.h
create mode 100644 libs/sra/libwsradb.vers.h
create mode 100644 libs/sra/libwsraschema.vers.h
create mode 100644 libs/sra/reader-abi.c
create mode 100644 libs/sra/reader-cmn.c
create mode 100644 libs/sra/reader-cmn.h
create mode 100644 libs/sra/reader-fastq.c
create mode 100644 libs/sra/reader-illumina.c
create mode 100644 libs/sra/reader-sff.c
create mode 100644 libs/sra/sra-debug.h
create mode 100644 libs/sra/sra-dflt-schema.c
create mode 100644 libs/sra/sra-priv.h
create mode 100644 libs/sra/sra-schema.c
create mode 100644 libs/sra/sracache.c
create mode 100644 libs/sra/sracol.c
create mode 100644 libs/sra/sramgr-cmn.c
create mode 100644 libs/sra/sramgr.c
create mode 100644 libs/sra/sraschema-priv.h
create mode 100644 libs/sra/sraschema-stub.c
create mode 100644 libs/sra/sraschema.c
create mode 100644 libs/sra/sratbl-cmn.c
create mode 100644 libs/sra/sratbl.c
create mode 100644 libs/sra/types.c
create mode 100644 libs/sra/wsramgr.c
create mode 100644 libs/sra/wsraschema-stub.c
create mode 100644 libs/sra/wsratbl.c
create mode 100644 libs/sraxf/.gitignore
create mode 100644 libs/sraxf/Makefile
create mode 100644 libs/sraxf/bio-start.c
create mode 100644 libs/sraxf/color-from-dna.c
create mode 100644 libs/sraxf/denormalize.c
create mode 100644 libs/sraxf/dna-from-color.c
create mode 100644 libs/sraxf/dynamic-454-read-descriptor.c
create mode 100644 libs/sraxf/extract-coordinates.c
create mode 100644 libs/sraxf/extract-name_coord.c
create mode 100644 libs/sraxf/extract-name_fmt.c
create mode 100644 libs/sraxf/extract-spot_name.c
create mode 100644 libs/sraxf/fix_read_seg_impl.h
create mode 100644 libs/sraxf/format-spot-name.c
create mode 100644 libs/sraxf/fpcodec.c
create mode 100644 libs/sraxf/index_lookup.c
create mode 100644 libs/sraxf/make-position.c
create mode 100644 libs/sraxf/name-tokenizer.h
create mode 100644 libs/sraxf/normalize.c
create mode 100644 libs/sraxf/prefix-tree-to-name.c
create mode 100644 libs/sraxf/process-position.c
create mode 100644 libs/sraxf/qstat-trigger.c
create mode 100644 libs/sraxf/qual4_codec.h
create mode 100644 libs/sraxf/qual4_decode.c
create mode 100644 libs/sraxf/qual4_encode.c
create mode 100644 libs/sraxf/read-desc.c
create mode 100644 libs/sraxf/read-seg-from-readn.c
create mode 100644 libs/sraxf/rewrite-spot-name.c
create mode 100644 libs/sraxf/rotate.c
create mode 100644 libs/sraxf/spot-desc.c
create mode 100644 libs/sraxf/stat_mod.c
create mode 100644 libs/sraxf/stat_mod.h
create mode 100644 libs/sraxf/stats.c
create mode 100644 libs/sraxf/stats_quality.c
create mode 100644 libs/sraxf/swap.c
create mode 100644 libs/sraxf/tokenize-spot_name-454.c
create mode 100644 libs/sraxf/tokenize-spot_name-abi.c
create mode 100644 libs/sraxf/tokenize-spot_name-generic-fastq.c
create mode 100644 libs/sraxf/tokenize-spot_name-helicos.c
create mode 100644 libs/sraxf/tokenize-spot_name-illumina.c
create mode 100644 libs/sraxf/tokenize-spot_name-ion-torrent.c
create mode 100644 libs/sraxf/untyped-priv.h
create mode 100644 libs/sraxf/untyped.c
create mode 100644 libs/sraxf/v0-decompress-init.c
create mode 100644 libs/sraxf/v0-decompress-local.h
create mode 100644 libs/sraxf/v0-decompress.c
create mode 100644 libs/sraxf/v0-decompress.h
create mode 100644 libs/sraxf/v0-funcs.c
create mode 100644 libs/sraxf/varloc.c
create mode 100644 libs/svdb/.gitignore
create mode 100644 libs/svdb/Makefile
create mode 100644 libs/svdb/svdb.c
create mode 100644 libs/tui/Makefile
create mode 100644 libs/tui/bsd/systui.c
create mode 100644 libs/tui/dir_dlg.c
create mode 100644 libs/tui/eventring.c
create mode 100644 libs/tui/eventring.h
create mode 100644 libs/tui/file_dlg.c
create mode 100644 libs/tui/line_policy.c
create mode 100644 libs/tui/line_policy.h
create mode 100644 libs/tui/linux/systui.c
create mode 100644 libs/tui/screen.c
create mode 100644 libs/tui/screen.h
create mode 100644 libs/tui/string_cache.c
create mode 100644 libs/tui/string_cache.h
create mode 100644 libs/tui/tui-priv.h
create mode 100644 libs/tui/tui.c
create mode 100644 libs/tui/tui_cpp.cpp
create mode 100644 libs/tui/tui_dlg.c
create mode 100644 libs/tui/tui_dlg_helper.c
create mode 100644 libs/tui/tui_menu.c
create mode 100644 libs/tui/tui_menu.h
create mode 100644 libs/tui/tui_palette.c
create mode 100644 libs/tui/tui_std_dlg.c
create mode 100644 libs/tui/tui_widget.c
create mode 100644 libs/tui/tui_widget.h
create mode 100644 libs/tui/tui_widget_button.c
create mode 100644 libs/tui/tui_widget_checkbox.c
create mode 100644 libs/tui/tui_widget_grid.c
create mode 100644 libs/tui/tui_widget_inputline.c
create mode 100644 libs/tui/tui_widget_label.c
create mode 100644 libs/tui/tui_widget_progress.c
create mode 100644 libs/tui/tui_widget_radiobox.c
create mode 100644 libs/tui/tui_widget_spin_edit.c
create mode 100644 libs/tui/tui_widget_string_list.c
create mode 100644 libs/tui/unix/systui.c
create mode 100644 libs/vdb/.gitignore
create mode 100644 libs/vdb/Makefile
create mode 100644 libs/vdb/blob-headers.c
create mode 100644 libs/vdb/blob-headers.h
create mode 100644 libs/vdb/blob-priv.h
create mode 100644 libs/vdb/blob.c
create mode 100644 libs/vdb/blob.h
create mode 100644 libs/vdb/cast.c
create mode 100644 libs/vdb/column-cmn.c
create mode 100644 libs/vdb/column-priv.h
create mode 100644 libs/vdb/column.c
create mode 100644 libs/vdb/compare.c
create mode 100644 libs/vdb/cursor-cmn.c
create mode 100644 libs/vdb/cursor-priv.h
create mode 100644 libs/vdb/cursor.c
create mode 100644 libs/vdb/database-cmn.c
create mode 100644 libs/vdb/database-depend.c
create mode 100644 libs/vdb/database-load.c
create mode 100644 libs/vdb/database-priv.h
create mode 100644 libs/vdb/database.c
create mode 100644 libs/vdb/dbmgr-cmn.c
create mode 100644 libs/vdb/dbmgr-priv.h
create mode 100644 libs/vdb/dbmgr.c
create mode 100644 libs/vdb/delta_average.c
create mode 100644 libs/vdb/environment-read.c
create mode 100644 libs/vdb/fixed-row-len.c
create mode 100644 libs/vdb/gen-cast.pl
create mode 100644 libs/vdb/index_insert.c
create mode 100644 libs/vdb/index_lookup.c
create mode 100644 libs/vdb/index_project.c
create mode 100644 libs/vdb/libvdb.vers.h
create mode 100644 libs/vdb/linker-cmn.c
create mode 100644 libs/vdb/linker-int.c
create mode 100644 libs/vdb/linker-priv.h
create mode 100644 libs/vdb/linker.c
create mode 100644 libs/vdb/merge.c
create mode 100644 libs/vdb/meta-append.c
create mode 100644 libs/vdb/meta-attr-read.c
create mode 100644 libs/vdb/meta-attr-write.c
create mode 100644 libs/vdb/meta-read.c
create mode 100644 libs/vdb/meta-value.c
create mode 100644 libs/vdb/meta-write.c
create mode 100644 libs/vdb/page-map.c
create mode 100644 libs/vdb/page-map.h
create mode 100644 libs/vdb/parameter-read.c
create mode 100644 libs/vdb/phys-cmn.c
create mode 100644 libs/vdb/phys-load.c
create mode 100644 libs/vdb/phys-priv.h
create mode 100644 libs/vdb/phys.c
create mode 100644 libs/vdb/prod-cmn.c
create mode 100644 libs/vdb/prod-expr.c
create mode 100644 libs/vdb/prod-expr.h
create mode 100644 libs/vdb/prod-func.c
create mode 100644 libs/vdb/prod-priv.h
create mode 100644 libs/vdb/prod.c
create mode 100644 libs/vdb/range-validate.c
create mode 100644 libs/vdb/redimension.c
create mode 100644 libs/vdb/report-vdb.c
create mode 100644 libs/vdb/row-id.c
create mode 100644 libs/vdb/row-len.c
create mode 100644 libs/vdb/schema-db.c
create mode 100644 libs/vdb/schema-dump.c
create mode 100644 libs/vdb/schema-dump.h
create mode 100644 libs/vdb/schema-eval.c
create mode 100644 libs/vdb/schema-expr.c
create mode 100644 libs/vdb/schema-expr.h
create mode 100644 libs/vdb/schema-func.c
create mode 100644 libs/vdb/schema-int.c
create mode 100644 libs/vdb/schema-parse.c
create mode 100644 libs/vdb/schema-parse.h
create mode 100644 libs/vdb/schema-priv.h
create mode 100644 libs/vdb/schema-prod.c
create mode 100644 libs/vdb/schema-tbl.c
create mode 100644 libs/vdb/schema-tok.c
create mode 100644 libs/vdb/schema-tok.h
create mode 100644 libs/vdb/schema-type.c
create mode 100644 libs/vdb/schema.c
create mode 100644 libs/vdb/split.c
create mode 100644 libs/vdb/table-cmn.c
create mode 100644 libs/vdb/table-load.c
create mode 100644 libs/vdb/table-priv.h
create mode 100644 libs/vdb/table.c
create mode 100644 libs/vdb/test/Makefile
create mode 100644 libs/vdb/test/test-prod-cmn.c
create mode 100644 libs/vdb/transpose.c
create mode 100644 libs/vdb/wcolumn.c
create mode 100644 libs/vdb/wcursor.c
create mode 100644 libs/vdb/wdatabase.c
create mode 100644 libs/vdb/wdbmgr.c
create mode 100644 libs/vdb/wlinker.c
create mode 100644 libs/vdb/wphys.c
create mode 100644 libs/vdb/wprod.c
create mode 100644 libs/vdb/wtable.c
create mode 100644 libs/vdb/xform-priv.h
create mode 100644 libs/vfs/Makefile
create mode 100644 libs/vfs/keyring.c
create mode 100644 libs/vfs/keyring.h
create mode 100644 libs/vfs/kurl-stub.c
create mode 100644 libs/vfs/manager.c
create mode 100644 libs/vfs/path-priv.h
create mode 100644 libs/vfs/path.c
create mode 100644 libs/vfs/resolver-3.0.c
create mode 100644 libs/vfs/resolver-priv.h
create mode 100644 libs/vfs/resolver.c
create mode 100644 libs/vfs/srapath-stub.c
create mode 100644 libs/vfs/srapath.c
create mode 100644 libs/vfs/unix/syskeyring.c
create mode 100644 libs/vfs/unix/syspath.c
create mode 100644 libs/vxf/.gitignore
create mode 100644 libs/vxf/Makefile
create mode 100644 libs/vxf/add-row-id.c
create mode 100644 libs/vxf/bit_or.c
create mode 100644 libs/vxf/bunzip.c
create mode 100644 libs/vxf/bzip.c
create mode 100644 libs/vxf/ceil.c
create mode 100644 libs/vxf/checksum.c
create mode 100644 libs/vxf/clip.c
create mode 100644 libs/vxf/cut.c
create mode 100644 libs/vxf/delta.c
create mode 100644 libs/vxf/deriv.c
create mode 100644 libs/vxf/diff.c
create mode 100644 libs/vxf/echo.c
create mode 100644 libs/vxf/entrez.c
create mode 100644 libs/vxf/exists.c
create mode 100644 libs/vxf/extract_token.c
create mode 100644 libs/vxf/floor.c
create mode 100644 libs/vxf/fsplit-join.impl.h
create mode 100644 libs/vxf/funzip.c
create mode 100644 libs/vxf/fzip.c
create mode 100644 libs/vxf/integral.c
create mode 100644 libs/vxf/integral_0.c
create mode 100644 libs/vxf/irzip.c
create mode 100644 libs/vxf/irzip.impl.h
create mode 100644 libs/vxf/iunzip.c
create mode 100644 libs/vxf/izip-common.h
create mode 100644 libs/vxf/izip-decode.impl.h
create mode 100644 libs/vxf/izip-encode.impl.h
create mode 100644 libs/vxf/izip.c
create mode 100644 libs/vxf/lower-case-tech-reads.c
create mode 100644 libs/vxf/map.c
create mode 100644 libs/vxf/math-funcs-impl.h
create mode 100644 libs/vxf/max.c
create mode 100644 libs/vxf/min.c
create mode 100644 libs/vxf/outlier-decoder.c
create mode 100644 libs/vxf/outlier-encoder.c
create mode 100644 libs/vxf/pack.c
create mode 100644 libs/vxf/paste.c
create mode 100644 libs/vxf/rand_4na_2na.c
create mode 100644 libs/vxf/rldecode.c
create mode 100644 libs/vxf/rlencode.c
create mode 100644 libs/vxf/round.c
create mode 100644 libs/vxf/simple-sub-select.c
create mode 100644 libs/vxf/sprintf.c
create mode 100644 libs/vxf/strtonum.c
create mode 100644 libs/vxf/subtract-row-id.c
create mode 100644 libs/vxf/sum.c
create mode 100644 libs/vxf/trim.c
create mode 100644 libs/vxf/trunc.c
create mode 100644 libs/vxf/undelta.c
create mode 100644 libs/vxf/unpack.c
create mode 100644 libs/vxf/unzip.c
create mode 100644 libs/vxf/vec-sum.c
create mode 100644 libs/vxf/wgs-tokenize-accession.c
create mode 100644 libs/vxf/zip.c
create mode 100644 libs/wgsxf/Makefile
create mode 100644 libs/wgsxf/build_read_type.c
create mode 100644 libs/wgsxf/build_scaffold.c
create mode 100644 libs/xfs/Makefile
create mode 100644 libs/xfs/bogus.c
create mode 100644 libs/xfs/common.h
create mode 100644 libs/xfs/contnode.c
create mode 100644 libs/xfs/contnode.h
create mode 100644 libs/xfs/doc.c
create mode 100644 libs/xfs/docnode.c
create mode 100644 libs/xfs/editors.c
create mode 100644 libs/xfs/encro.c
create mode 100644 libs/xfs/encws.c
create mode 100644 libs/xfs/foo.c
create mode 100644 libs/xfs/gap.c
create mode 100644 libs/xfs/gapc.c
create mode 100644 libs/xfs/gapf.c
create mode 100644 libs/xfs/gapk.c
create mode 100644 libs/xfs/gapka.c
create mode 100644 libs/xfs/gapks.c
create mode 100644 libs/xfs/handle.c
create mode 100644 libs/xfs/http.c
create mode 100644 libs/xfs/kfs.c
create mode 100644 libs/xfs/lockdpt.c
create mode 100644 libs/xfs/lockdpt.h
create mode 100644 libs/xfs/lreader.c
create mode 100644 libs/xfs/lreader.h
create mode 100644 libs/xfs/mehr.c
create mode 100644 libs/xfs/mehr.h
create mode 100644 libs/xfs/model.c
create mode 100644 libs/xfs/ncon.c
create mode 100644 libs/xfs/ncon.h
create mode 100644 libs/xfs/node.c
create mode 100644 libs/xfs/owp.c
create mode 100644 libs/xfs/owp.h
create mode 100644 libs/xfs/path.c
create mode 100644 libs/xfs/perm.c
create mode 100644 libs/xfs/platform.h
create mode 100644 libs/xfs/readme.c
create mode 100644 libs/xfs/schwarzschraube.c
create mode 100644 libs/xfs/schwarzschraube.h
create mode 100644 libs/xfs/simcon.c
create mode 100644 libs/xfs/spen.c
create mode 100644 libs/xfs/spen.h
create mode 100644 libs/xfs/tar.c
create mode 100644 libs/xfs/teleport.c
create mode 100644 libs/xfs/teleport.h
create mode 100644 libs/xfs/tree.c
create mode 100644 libs/xfs/unix/operations.c
create mode 100644 libs/xfs/unix/operations.h
create mode 100644 libs/xfs/unix/platform.c
create mode 100644 libs/xfs/unix/security.c
create mode 100644 libs/xfs/xencro.c
create mode 100644 libs/xfs/xencro.h
create mode 100644 libs/xfs/xencws.c
create mode 100644 libs/xfs/xencws.h
create mode 100644 libs/xfs/xfs-priv.h
create mode 100644 libs/xfs/xfs.c
create mode 100644 libs/xfs/xgap.c
create mode 100644 libs/xfs/xgap.h
create mode 100644 libs/xfs/xgapf.c
create mode 100644 libs/xfs/xgapf.h
create mode 100644 libs/xfs/xgapk.c
create mode 100644 libs/xfs/xgapk.h
create mode 100644 libs/xfs/xhttp.c
create mode 100644 libs/xfs/xhttp.h
create mode 100644 libs/xfs/xlog.c
create mode 100644 libs/xfs/xtar.c
create mode 100644 libs/xfs/xtar.h
create mode 100644 libs/xfs/zehr.c
create mode 100644 libs/xfs/zehr.h
create mode 100755 local-builds.sh
create mode 100755 schema_crc.pl
delete mode 100755 scripts/explain_sam_flags.py
delete mode 100755 scripts/release_picard.sh
create mode 100755 setup/install
create mode 100644 setup/install.perl
create mode 100644 setup/install.prl
create mode 100644 setup/konfigure.perl
create mode 100644 setup/os-arch.perl
create mode 100644 setup/os-arch.prl
create mode 100644 setup/package.prl
create mode 100755 setup/s/install
create mode 100644 setup/s/os.prl
delete mode 100644 src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/AlignmentBlock.java
delete mode 100644 src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMFileConstants.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMFileReader.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMFileSpan.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMFileWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMIndexContent.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMIndexMetaData.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMIndexWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMIndexer.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMIteratorFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/BAMRecordCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/BamFileIoUtils.java
delete mode 100644 src/main/java/htsjdk/samtools/BamIndexValidator.java
delete mode 100644 src/main/java/htsjdk/samtools/Bin.java
delete mode 100644 src/main/java/htsjdk/samtools/BinList.java
delete mode 100644 src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/BinaryCigarCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/BinaryTagCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/BinningIndexBuilder.java
delete mode 100644 src/main/java/htsjdk/samtools/BinningIndexContent.java
delete mode 100644 src/main/java/htsjdk/samtools/BrowseableBAMIndex.java
delete mode 100755 src/main/java/htsjdk/samtools/CRAMBAIIndexer.java
delete mode 100644 src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java
delete mode 100644 src/main/java/htsjdk/samtools/CRAMContainerStreamWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/CRAMFileReader.java
delete mode 100644 src/main/java/htsjdk/samtools/CRAMFileWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/CRAMIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/CachingBAMFileIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/ChainedDownsamplingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/Chunk.java
delete mode 100644 src/main/java/htsjdk/samtools/Cigar.java
delete mode 100644 src/main/java/htsjdk/samtools/CigarElement.java
delete mode 100644 src/main/java/htsjdk/samtools/CigarOperator.java
delete mode 100644 src/main/java/htsjdk/samtools/ComparableSamRecordIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/ConstantMemoryDownsamplingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java
delete mode 100644 src/main/java/htsjdk/samtools/CustomReaderFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/DefaultSAMRecordFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/Defaults.java
delete mode 100644 src/main/java/htsjdk/samtools/DiskBasedBAMFileIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/DownsamplingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java
delete mode 100644 src/main/java/htsjdk/samtools/DuplicateSet.java
delete mode 100644 src/main/java/htsjdk/samtools/DuplicateSetIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/FileTruncatedException.java
delete mode 100755 src/main/java/htsjdk/samtools/FixBAMFile.java
delete mode 100644 src/main/java/htsjdk/samtools/GenomicIndexUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/HighAccuracyDownsamplingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/LinearIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/MergingSamRecordIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/NotPrimarySkippingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/QueryInterval.java
delete mode 100644 src/main/java/htsjdk/samtools/ReservedTagConstants.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMBinaryTagAndValue.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMException.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFileHeader.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFileSource.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFileSpan.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFileWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFileWriterFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFileWriterImpl.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFlag.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMFormatException.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMHeaderRecordComparator.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMLineParser.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMProgramRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMReadGroupRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordComparator.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordDuplicateComparator.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordFactory.java
delete mode 100755 src/main/java/htsjdk/samtools/SAMRecordIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordQueryHashComparator.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMRecordUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMSequenceDictionary.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMSequenceDictionaryCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMSequenceRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMSortOrderChecker.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMTag.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMTagUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMTestUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMTextReader.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMTextWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMTools.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMUtils.java
delete mode 100644 src/main/java/htsjdk/samtools/SAMValidationError.java
delete mode 100644 src/main/java/htsjdk/samtools/SQTagUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/SRAFileReader.java
delete mode 100644 src/main/java/htsjdk/samtools/SRAIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/SRAIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/SamFileHeaderMerger.java
delete mode 100644 src/main/java/htsjdk/samtools/SamFileValidator.java
delete mode 100644 src/main/java/htsjdk/samtools/SamFiles.java
delete mode 100644 src/main/java/htsjdk/samtools/SamFlagField.java
delete mode 100644 src/main/java/htsjdk/samtools/SamIndexes.java
delete mode 100644 src/main/java/htsjdk/samtools/SamInputResource.java
delete mode 100644 src/main/java/htsjdk/samtools/SamPairUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/SamReader.java
delete mode 100644 src/main/java/htsjdk/samtools/SamReaderFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/SamStreams.java
delete mode 100644 src/main/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/StreamInflatingIndexingOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/TagValueAndUnsignedArrayFlag.java
delete mode 100755 src/main/java/htsjdk/samtools/TextCigarCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/TextTagCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/TextualBAMIndexWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/ValidationStringency.java
delete mode 100644 src/main/java/htsjdk/samtools/apps/TimeChannel.java
delete mode 100644 src/main/java/htsjdk/samtools/apps/TimeRandomAccessFile.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/CRAIEntry.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/CRAIIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/CRAMException.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/ContainerParser.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/Cram2SamRecordFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/CramIO.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/CramNormalizer.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/Sam2CramRecordFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/build/Utils.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/common/CramVersionPolicies.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/common/CramVersions.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/common/IntHashMap.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/common/MutableInt.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/common/Version.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/AbstractSerialDigest.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/ByteSumCombine.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/Combine.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/ContentDigests.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/Crc32Hasher.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/IntegerSumCombine.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/MessageDigestHasher.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/digest/SERIES.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/AbstractBitCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/BetaIntegerCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/BetaIntegerEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/BitCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ByteArrayStopEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/DataSeries.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/DataSeriesMap.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/DataSeriesType.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/Encoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/EncodingFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalByteArrayCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalByteArrayEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalByteCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalByteEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalCompressor.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalIntegerCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalIntegerEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalLongCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/ExternalLongEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GammaIntegerCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GammaIntegerEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GolombIntegerCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GolombIntegerEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GolombLongCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GolombLongEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GolombRiceIntegerCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/GolombRiceIntegerEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/NullCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/NullEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/SubexponentialIntegerCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/SubexponentialIntegerEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanCode.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanLeaf.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanNode.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanTree.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/CanonicalHuffmanByteCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/CanonicalHuffmanIntegerCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanBitCode.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteHelper.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntHelper.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntegerEncoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanParamsCalculator.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/Constants.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/D04.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/D14.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/Decoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/E04.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/E14.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/Encoding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/Frequencies.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/RANS.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/rans/Utils.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/reader/AbstractReader.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/reader/CramRecordReader.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/reader/DataReader.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/reader/RefSeqIdReader.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Bases.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Deletion.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/HardClip.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Insertion.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Padding.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Scores.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Substitution.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/writer/DataWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/writer/DataWriterFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/encoding/writer/Writer.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/BitInputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/BitOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/CRC32InputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/CRC32OutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/CountingInputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/CramArray.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/CramInt.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/DefaultBitInputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/DefaultBitOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/ExposedByteArrayOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/ExternalCompression.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/ITF8.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/InputStreamUtils.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/io/LTF8.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/BaseCategory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/BaseCategoryType.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/Binning.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/PreservationPolicy.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/QualityScorePreservation.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/QualityScoreTreatment.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/QualityScoreTreatmentType.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/ReadCategory.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/lossy/ReadCategoryType.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/ref/CRAMReferenceSource.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/ref/EnaRefService.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/ref/InMemoryReferenceSequenceFile.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/ref/ReferenceRegion.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/ref/ReferenceSource.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/ref/ReferenceTracks.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/AlignmentSpan.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/Block.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/BlockCompressionMethod.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/BlockContentType.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/Container.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/ContainerHeaderIO.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/ContainerIO.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/CramCompressionRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/CramHeader.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/EncodingID.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/EncodingKey.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/EncodingParams.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/ReadTag.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/Slice.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/SliceIO.java
delete mode 100644 src/main/java/htsjdk/samtools/cram/structure/SubstitutionMatrix.java
delete mode 100644 src/main/java/htsjdk/samtools/example/ExampleSamUsage.java
delete mode 100755 src/main/java/htsjdk/samtools/example/PrintReadsExample.java
delete mode 100644 src/main/java/htsjdk/samtools/fastq/AsyncFastqWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/fastq/BasicFastqWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/fastq/FastqConstants.java
delete mode 100755 src/main/java/htsjdk/samtools/fastq/FastqReader.java
delete mode 100755 src/main/java/htsjdk/samtools/fastq/FastqRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/fastq/FastqWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/fastq/FastqWriterFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/AggregateFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/AlignedFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/DuplicateReadFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/FailsVendorReadQualityFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/FilteringIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/FilteringSamIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/InsertSizeFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/IntervalFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/JavascriptSamRecordFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/MappingQualityFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/OverclippedReadFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/ReadNameFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/SamRecordFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/SecondaryAlignmentFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/SolexaNoiseFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/TagFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/filter/WholeReadClippedFilter.java
delete mode 100644 src/main/java/htsjdk/samtools/liftover/Chain.java
delete mode 100644 src/main/java/htsjdk/samtools/liftover/LiftOver.java
delete mode 100644 src/main/java/htsjdk/samtools/metrics/Header.java
delete mode 100644 src/main/java/htsjdk/samtools/metrics/MetricBase.java
delete mode 100644 src/main/java/htsjdk/samtools/metrics/MetricsFile.java
delete mode 100644 src/main/java/htsjdk/samtools/metrics/StringHeader.java
delete mode 100644 src/main/java/htsjdk/samtools/metrics/VersionHeader.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/AbstractFastaSequenceFile.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/FastaSequenceFile.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/FastaSequenceIndex.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/IndexedFastaSequenceFile.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/ReferenceSequence.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/ReferenceSequenceFile.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileWalker.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/ByteArraySeekableStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableBufferedStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableFileStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableMemoryStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableStream.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/seekablestream/UserPasswordInput.java
delete mode 100644 src/main/java/htsjdk/samtools/sra/ReferenceCache.java
delete mode 100644 src/main/java/htsjdk/samtools/sra/SRAAccession.java
delete mode 100644 src/main/java/htsjdk/samtools/sra/SRAAlignmentIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/sra/SRAIndexedSequenceFile.java
delete mode 100644 src/main/java/htsjdk/samtools/sra/SRALazyRecord.java
delete mode 100644 src/main/java/htsjdk/samtools/sra/SRAUnalignmentIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/sra/SRAUtils.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AbstractAsyncWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AbstractIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AbstractLocusInfo.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AsciiWriter.java
delete mode 100644 src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/BinaryCodec.java
delete mode 100644 src/main/java/htsjdk/samtools/util/BlockCompressedFilePointerUtil.java
delete mode 100755 src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/util/BlockCompressedStreamConstants.java
delete mode 100644 src/main/java/htsjdk/samtools/util/BlockGunzipper.java
delete mode 100644 src/main/java/htsjdk/samtools/util/BufferedLineReader.java
delete mode 100644 src/main/java/htsjdk/samtools/util/CigarUtil.java
delete mode 100755 src/main/java/htsjdk/samtools/util/CloseableIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/CloserUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/CodeUtil.java
delete mode 100755 src/main/java/htsjdk/samtools/util/CollectionUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ComparableTuple.java
delete mode 100644 src/main/java/htsjdk/samtools/util/CoordMath.java
delete mode 100644 src/main/java/htsjdk/samtools/util/CoordSpanInputSteam.java
delete mode 100644 src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/util/DateParser.java
delete mode 100644 src/main/java/htsjdk/samtools/util/DelegatingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/DiskBackedQueue.java
delete mode 100644 src/main/java/htsjdk/samtools/util/EdgeReadIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java
delete mode 100644 src/main/java/htsjdk/samtools/util/FastLineReader.java
delete mode 100644 src/main/java/htsjdk/samtools/util/FastqQualityFormat.java
delete mode 100644 src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java
delete mode 100644 src/main/java/htsjdk/samtools/util/FormatUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Histogram.java
delete mode 100644 src/main/java/htsjdk/samtools/util/HttpUtils.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IOUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Interval.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IntervalList.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IntervalTree.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IntervalTreeMap.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IntervalUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Iso8601Date.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IterableAdapter.java
delete mode 100644 src/main/java/htsjdk/samtools/util/IterableOnceIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Iterables.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Lazy.java
delete mode 100644 src/main/java/htsjdk/samtools/util/LineReader.java
delete mode 100755 src/main/java/htsjdk/samtools/util/ListMap.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Locatable.java
delete mode 100644 src/main/java/htsjdk/samtools/util/LocationAware.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Locus.java
delete mode 100644 src/main/java/htsjdk/samtools/util/LocusComparator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/LocusImpl.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Log.java
delete mode 100755 src/main/java/htsjdk/samtools/util/Md5CalculatingInputStream.java
delete mode 100755 src/main/java/htsjdk/samtools/util/Md5CalculatingOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/util/MergingIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Murmur3.java
delete mode 100644 src/main/java/htsjdk/samtools/util/OverlapDetector.java
delete mode 100644 src/main/java/htsjdk/samtools/util/PeekIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/PeekableIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/PositionalOutputStream.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ProcessExecutor.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ProgressLogger.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ProgressLoggerInterface.java
delete mode 100644 src/main/java/htsjdk/samtools/util/QualityEncodingDetector.java
delete mode 100644 src/main/java/htsjdk/samtools/util/QualityUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ReferenceSequenceMask.java
delete mode 100644 src/main/java/htsjdk/samtools/util/RelativeIso8601Date.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ResourceLimitedMap.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ResourceLimitedMapFunctor.java
delete mode 100644 src/main/java/htsjdk/samtools/util/RuntimeEOFException.java
delete mode 100644 src/main/java/htsjdk/samtools/util/RuntimeIOException.java
delete mode 100644 src/main/java/htsjdk/samtools/util/RuntimeScriptException.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SamLocusIterator.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SamRecordTrackingBuffer.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SamRecordWithOrdinal.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SequenceUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SnappyLoader.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SolexaQualityConverter.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SortingCollection.java
delete mode 100644 src/main/java/htsjdk/samtools/util/SortingLongCollection.java
delete mode 100644 src/main/java/htsjdk/samtools/util/StopWatch.java
delete mode 100644 src/main/java/htsjdk/samtools/util/StringLineReader.java
delete mode 100644 src/main/java/htsjdk/samtools/util/StringUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/TempStreamFactory.java
delete mode 100644 src/main/java/htsjdk/samtools/util/TestUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/TrimmingUtil.java
delete mode 100644 src/main/java/htsjdk/samtools/util/Tuple.java
delete mode 100644 src/main/java/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ftp/FTPClient.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ftp/FTPReply.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ftp/FTPStream.java
delete mode 100644 src/main/java/htsjdk/samtools/util/ftp/FTPUtils.java
delete mode 100644 src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java
delete mode 100644 src/main/java/htsjdk/tribble/AbstractFeatureCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/AbstractFeatureReader.java
delete mode 100644 src/main/java/htsjdk/tribble/AsciiFeatureCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/BinaryFeatureCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/CloseableTribbleIterator.java
delete mode 100644 src/main/java/htsjdk/tribble/Feature.java
delete mode 100644 src/main/java/htsjdk/tribble/FeatureCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/FeatureCodecHeader.java
delete mode 100644 src/main/java/htsjdk/tribble/FeatureReader.java
delete mode 100755 src/main/java/htsjdk/tribble/NameAwareCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/SimpleFeature.java
delete mode 100644 src/main/java/htsjdk/tribble/TabixFeatureReader.java
delete mode 100644 src/main/java/htsjdk/tribble/Tribble.java
delete mode 100644 src/main/java/htsjdk/tribble/TribbleException.java
delete mode 100644 src/main/java/htsjdk/tribble/TribbleIndexedFeatureReader.java
delete mode 100644 src/main/java/htsjdk/tribble/annotation/Strand.java
delete mode 100644 src/main/java/htsjdk/tribble/bed/BEDCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/bed/BEDFeature.java
delete mode 100644 src/main/java/htsjdk/tribble/bed/FullBEDFeature.java
delete mode 100644 src/main/java/htsjdk/tribble/bed/SimpleBEDFeature.java
delete mode 100644 src/main/java/htsjdk/tribble/example/CountRecords.java
delete mode 100644 src/main/java/htsjdk/tribble/example/ExampleBinaryCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/example/IndexToTable.java
delete mode 100644 src/main/java/htsjdk/tribble/example/IndicesAreEqual.java
delete mode 100644 src/main/java/htsjdk/tribble/example/ProfileIndexReading.java
delete mode 100644 src/main/java/htsjdk/tribble/exception/CodecLineParsingException.java
delete mode 100644 src/main/java/htsjdk/tribble/exception/UnsortedFileException.java
delete mode 100644 src/main/java/htsjdk/tribble/gelitext/DiploidGenotype.java
delete mode 100644 src/main/java/htsjdk/tribble/gelitext/GeliTextCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/gelitext/GeliTextFeature.java
delete mode 100644 src/main/java/htsjdk/tribble/index/AbstractIndex.java
delete mode 100644 src/main/java/htsjdk/tribble/index/Block.java
delete mode 100644 src/main/java/htsjdk/tribble/index/ChrIndex.java
delete mode 100644 src/main/java/htsjdk/tribble/index/DynamicIndexCreator.java
delete mode 100644 src/main/java/htsjdk/tribble/index/Index.java
delete mode 100644 src/main/java/htsjdk/tribble/index/IndexCreator.java
delete mode 100644 src/main/java/htsjdk/tribble/index/IndexFactory.java
delete mode 100644 src/main/java/htsjdk/tribble/index/MutableIndex.java
delete mode 100644 src/main/java/htsjdk/tribble/index/TribbleIndexCreator.java
delete mode 100644 src/main/java/htsjdk/tribble/index/interval/Interval.java
delete mode 100644 src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java
delete mode 100644 src/main/java/htsjdk/tribble/index/interval/IntervalTree.java
delete mode 100644 src/main/java/htsjdk/tribble/index/interval/IntervalTreeIndex.java
delete mode 100644 src/main/java/htsjdk/tribble/index/linear/LinearIndex.java
delete mode 100644 src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java
delete mode 100644 src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java
delete mode 100644 src/main/java/htsjdk/tribble/index/tabix/TabixIndex.java
delete mode 100644 src/main/java/htsjdk/tribble/index/tabix/TabixIndexCreator.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/AsciiLineReader.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/AsciiLineReaderIterator.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/LineIterator.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/LineIteratorImpl.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/LineReader.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/LineReaderUtil.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/Positional.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/PositionalBufferedStream.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/SynchronousLineReader.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/TabixIteratorLineReader.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/TabixReader.java
delete mode 100644 src/main/java/htsjdk/tribble/readme.txt
delete mode 100644 src/main/java/htsjdk/tribble/util/FTPHelper.java
delete mode 100644 src/main/java/htsjdk/tribble/util/HTTPHelper.java
delete mode 100644 src/main/java/htsjdk/tribble/util/LittleEndianInputStream.java
delete mode 100644 src/main/java/htsjdk/tribble/util/LittleEndianOutputStream.java
delete mode 100644 src/main/java/htsjdk/tribble/util/MathUtils.java
delete mode 100644 src/main/java/htsjdk/tribble/util/ParsingUtils.java
delete mode 100644 src/main/java/htsjdk/tribble/util/RemoteURLHelper.java
delete mode 100644 src/main/java/htsjdk/tribble/util/TabixUtils.java
delete mode 100644 src/main/java/htsjdk/tribble/util/URLHelper.java
delete mode 100755 src/main/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.java
delete mode 100644 src/main/java/htsjdk/variant/bcf2/BCF2Codec.java
delete mode 100644 src/main/java/htsjdk/variant/bcf2/BCF2Decoder.java
delete mode 100644 src/main/java/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.java
delete mode 100644 src/main/java/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.java
delete mode 100644 src/main/java/htsjdk/variant/bcf2/BCF2Type.java
delete mode 100644 src/main/java/htsjdk/variant/bcf2/BCF2Utils.java
delete mode 100644 src/main/java/htsjdk/variant/bcf2/BCFVersion.java
delete mode 100755 src/main/java/htsjdk/variant/example/PrintVariantsExample.java
delete mode 100644 src/main/java/htsjdk/variant/utils/GeneralUtils.java
delete mode 100644 src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/Allele.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/CommonInfo.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/FastGenotype.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/Genotype.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/GenotypeJEXLContext.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/GenotypeType.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/JEXLMap.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/JexlMissingValueTreatment.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/LazyGenotypesContext.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/StructuralVariantType.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/VariantContext.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/VariantJEXLContext.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/CompoundFilter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/FilteringIterator.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/PassingVariantFilter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/SnpFilter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/filter/VariantContextFilter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/BCF2Encoder.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/BCF2Writer.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/IndexingVariantContextWriter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/Options.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/VCFWriter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriter.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterFactory.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/AbstractVCFCodec.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCF3Codec.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFCodec.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFConstants.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFContigHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFEncoder.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFFileReader.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFFormatHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFHeader.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFHeaderLineCount.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFHeaderLineTranslator.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFHeaderLineType.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFHeaderVersion.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFIDHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFInfoHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFRecordCodec.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java
delete mode 100644 src/main/java/htsjdk/variant/vcf/VCFUtils.java
delete mode 100644 src/test/java/htsjdk/cram/io/ExternalCompressionTest.java
delete mode 100644 src/test/java/htsjdk/samtools/AbstractBAMFileIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java
delete mode 100755 src/test/java/htsjdk/samtools/BAMFileIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/BAMFileWriterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/BAMIndexWriterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/BAMIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
delete mode 100644 src/test/java/htsjdk/samtools/BinTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMBAIIndexerTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMComplianceTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMContainerStreamWriterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMEdgeCasesTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMFileBAIIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMFileCRAIIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMFileReaderTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMFileWriterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMFileWriterWithIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CRAMIndexQueryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/ChunkTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CigarCodecTest.java
delete mode 100644 src/test/java/htsjdk/samtools/CigarTest.java
delete mode 100644 src/test/java/htsjdk/samtools/DownsamplingIteratorTests.java
delete mode 100644 src/test/java/htsjdk/samtools/DuplicateSetIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/GenomicIndexUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/MergingSamRecordIteratorGroupCollisionTest.java
delete mode 100644 src/test/java/htsjdk/samtools/MergingSamRecordIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/ProgramRecordChainingTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMCloneTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMFileWriterFactoryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMFlagTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMIntegerTagTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMRecordDuplicateComparatorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMRecordUnitTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMSequenceDictionaryCodecTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMTextReaderTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMTextWriterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SAMUtilsTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamFileHeaderMergerTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamFilesTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamFlagFieldTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamHeaderRecordComparatorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamIndexesTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamPairUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
delete mode 100755 src/test/java/htsjdk/samtools/SamReaderSortTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamReaderTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamSpecIntTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SamStreamsTest.java
delete mode 100644 src/test/java/htsjdk/samtools/SequenceNameTruncationAndValidationTest.java
delete mode 100644 src/test/java/htsjdk/samtools/ValidateSamFileTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/CRAIEntryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/CRAIIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/LosslessRoundTripTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/VersionTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/build/CompressionHeaderFactoryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/build/ContainerFactoryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/build/ContainerParserTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/build/CramIOTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/encoding/rans/RansTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/io/ITF8Test.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/io/LTF8Test.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/lossy/QualityScorePreservationTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/structure/CramCompressionRecordTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/structure/ReadTagTest.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/structure/SliceTests.java
delete mode 100644 src/test/java/htsjdk/samtools/cram/structure/SubstitutionMatrixTest.java
delete mode 100644 src/test/java/htsjdk/samtools/fastq/FastqRecordTest.java
delete mode 100644 src/test/java/htsjdk/samtools/fastq/FastqWriterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/FailsVendorReadQualityFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/InsertSizeFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/JavascriptSamRecordFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/MappingQualityFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/OverclippedReadFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/SolexaNoiseFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/filter/TagFilterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/liftover/LiftOverTest.java
delete mode 100644 src/test/java/htsjdk/samtools/metrics/MetricBaseTest.java
delete mode 100644 src/test/java/htsjdk/samtools/metrics/MetricsFileTest.java
delete mode 100644 src/test/java/htsjdk/samtools/metrics/StringHeaderTest.java
delete mode 100644 src/test/java/htsjdk/samtools/metrics/VersionHeaderTest.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/FakeReferenceSequenceFile.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/FastaSequenceFileTest.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/FastaSequenceIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/InMemoryReferenceSequenceFile.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/IndexedFastaSequenceFileTest.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileFactoryTests.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileWalkerTest.java
delete mode 100644 src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java
delete mode 100644 src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/seekablestream/SeekableFileStreamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/seekablestream/SeekableMemoryStreamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/seekablestream/SeekablePathStreamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/sra/AbstractSRATest.java
delete mode 100644 src/test/java/htsjdk/samtools/sra/SRAAccessionTest.java
delete mode 100644 src/test/java/htsjdk/samtools/sra/SRAIndexTest.java
delete mode 100644 src/test/java/htsjdk/samtools/sra/SRALazyRecordTest.java
delete mode 100644 src/test/java/htsjdk/samtools/sra/SRAQueryTest.java
delete mode 100644 src/test/java/htsjdk/samtools/sra/SRAReferenceTest.java
delete mode 100644 src/test/java/htsjdk/samtools/sra/SRATest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/AbstractLocusInfoTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/AbstractLocusIteratorTestTemplate.java
delete mode 100644 src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/AsyncWriterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/BinaryCodecTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/BlockCompressedFilePointerUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/BlockCompressedOutputStreamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/BlockCompressedTerminatorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/CigarUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/CloseableIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/CodeUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/ComparableTupleTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/CoordSpanInputSteamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/DiskBackedQueueTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/HistogramTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/IntervalListTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/IntervalTreeMapTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/IntervalTreeTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/IoUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/Iso8601DateTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/IupacTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/MergingIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/OverlapDetectorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/PositionalOutputStreamTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/QualityEncodingDetectorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/RelativeIso8601DateTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/SequenceUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/SolexaQualityConverterTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/SortingCollectionTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/SortingLongCollectionTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/StringLineReaderTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/StringUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/TrimmingUtilTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/TupleTest.java
delete mode 100644 src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
delete mode 100644 src/test/java/htsjdk/tribble/BinaryFeaturesTest.java
delete mode 100644 src/test/java/htsjdk/tribble/FeatureReaderTest.java
delete mode 100644 src/test/java/htsjdk/tribble/TestUtils.java
delete mode 100644 src/test/java/htsjdk/tribble/TribbleIndexFeatureReaderTest.java
delete mode 100644 src/test/java/htsjdk/tribble/TribbleTest.java
delete mode 100644 src/test/java/htsjdk/tribble/bed/BEDCodecTest.java
delete mode 100644 src/test/java/htsjdk/tribble/gelitext/GeliTextTest.java
delete mode 100644 src/test/java/htsjdk/tribble/index/IndexFactoryTest.java
delete mode 100644 src/test/java/htsjdk/tribble/index/IndexTest.java
delete mode 100644 src/test/java/htsjdk/tribble/index/interval/IntervalTreeTest.java
delete mode 100644 src/test/java/htsjdk/tribble/index/linear/LinearIndexTest.java
delete mode 100644 src/test/java/htsjdk/tribble/index/tabix/TabixIndexTest.java
delete mode 100644 src/test/java/htsjdk/tribble/readers/AsciiLineReaderTest.java
delete mode 100644 src/test/java/htsjdk/tribble/readers/LongLineBufferedReaderTest.java
delete mode 100644 src/test/java/htsjdk/tribble/readers/PositionalBufferedStreamTest.java
delete mode 100644 src/test/java/htsjdk/tribble/readers/ReaderTest.java
delete mode 100644 src/test/java/htsjdk/tribble/readers/SynchronousLineReaderUnitTest.java
delete mode 100644 src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
delete mode 100644 src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
delete mode 100644 src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
delete mode 100644 src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
delete mode 100644 src/test/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculationTest.java
delete mode 100644 src/test/java/htsjdk/variant/PrintVariantsExampleTest.java
delete mode 100644 src/test/java/htsjdk/variant/VariantBaseTest.java
delete mode 100644 src/test/java/htsjdk/variant/bcf2/BCF2EncoderDecoderUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/bcf2/BCF2UtilsUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractorTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/AlleleUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/GenotypeBuilderTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/GenotypeUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/GenotypesContextUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/VariantContextBuilderTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/VariantContextTestProvider.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/VariantJEXLContextUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/AllFailFilter.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/AllPassFilter.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/CompoundFilterTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIteratorTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilterTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilterTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/PassingVariantFilterTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/writer/VCFWriterUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWritersUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/AbstractVCFCodecTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/IndexFactoryUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/VCFCompoundHeaderLineUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/VCFHeaderLineTranslatorUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/VCFHeaderLineUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
delete mode 100644 src/test/java/htsjdk/variant/vcf/VCFStandardHeaderLinesUnitTest.java
delete mode 100755 src/test/resources/htsjdk/samtools/BAMCigarOverflowTest/CigarOverflowTest.bam
delete mode 100644 src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam
delete mode 100644 src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai
delete mode 120000 src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam
delete mode 120000 src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam.bai
delete mode 120000 src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam
delete mode 100755 src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.bam
delete mode 100644 src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.sam
delete mode 100755 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome1to10.bam
delete mode 100755 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome5to9.bam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file1.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file2.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/expected_output.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file1.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file2.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file3.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file4.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/expected_output.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/1.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/2.sam
delete mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.dict
delete mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/upper_and_lowercase_read.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/bad_index.bai
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/bad_index.bam
delete mode 100755 src/test/resources/htsjdk/samtools/ValidateSamFileTest/buggyHeader.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicate_rg.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicated_reads.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicated_reads_out_of_order.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/hanging_tab.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/inappropriate_mate_cigar_string.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_coord_sort_order.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_mate_cigar_string.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_platform_unit.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_queryname_sort_order.sam
delete mode 100755 src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_no_oqs.sam
delete mode 100755 src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_oqs.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_fields.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_platform_unit.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/test_samfile_version_1pt5.bam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated.bam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated_quals.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated_tag.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/valid.sam
delete mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/zero_length_read.sam
delete mode 100644 src/test/resources/htsjdk/samtools/block_compressed.sam.gz
delete mode 100644 src/test/resources/htsjdk/samtools/compressed.bam
delete mode 100644 src/test/resources/htsjdk/samtools/compressed.sam.gz
delete mode 100755 src/test/resources/htsjdk/samtools/coordinate_sorted.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram.bai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.dict
delete mode 100644 src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram.crai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram.crai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram.crai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf#values.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf#values.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf#values.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#bounds.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#bounds.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#bounds.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#clip.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#clip.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#clip.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#noseq.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#noseq.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#noseq.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad1.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad1.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad1.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad2.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad2.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad2.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad3.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad3.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#pad3.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#unknown.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#unknown.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1#unknown.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c1.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c2#pad.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/c2#pad.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#1.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#1.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#1.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#2.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#2.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#2.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#5.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#5.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#5.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#5b.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#5b.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#5b.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#large_seq.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#large_seq.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#large_seq.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#supp.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#supp.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#supp.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#tag_padded.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#tag_padded.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#tag_padded.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap1.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap1.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap1.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap2.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap2.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce#unmap2.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/ce.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram.bai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram.bai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram.crai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/fieldarith.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.dict
delete mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.dict
delete mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/io/bzip2-test.bz2
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.cram.bai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.dict
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.dict
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#blank.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#blank.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#large_aux.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#large_aux.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#large_aux.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#large_aux2.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#large_aux2.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#large_aux2.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#minimal.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#minimal.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#minimal.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#pair.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#pair.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#pair.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#rg.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#rg.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#rg.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#tlen.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#tlen.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#tlen2.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#tlen2.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#triplet.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#triplet.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#triplet.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#unsorted.2.1.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#unsorted.3.0.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx#unsorted.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/xx.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram_query_sorted.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram_query_sorted.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/cram_query_sorted.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram_tlen.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/cram_tlen.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram_tlen_reads.sorted.sam
delete mode 100644 src/test/resources/htsjdk/samtools/cram_with_bai_index.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram_with_bai_index.cram.bai
delete mode 100644 src/test/resources/htsjdk/samtools/cram_with_crai_index.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram_with_crai_index.cram.crai
delete mode 100755 src/test/resources/htsjdk/samtools/empty.bai
delete mode 100644 src/test/resources/htsjdk/samtools/empty.bam
delete mode 100755 src/test/resources/htsjdk/samtools/empty_no_empty_gzip_block.bai
delete mode 100644 src/test/resources/htsjdk/samtools/empty_no_empty_gzip_block.bam
delete mode 100644 src/test/resources/htsjdk/samtools/hg19mini.dict
delete mode 100644 src/test/resources/htsjdk/samtools/hg19mini.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/hg19mini.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTest.vcf
delete mode 100644 src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list
delete mode 100644 src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverse.interval_list
delete mode 100644 src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list
delete mode 100644 src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf
delete mode 100644 src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestManualComp.interval_list
delete mode 100644 src/test/resources/htsjdk/samtools/intervallist/IntervalListchr123_empty.interval_list
delete mode 100644 src/test/resources/htsjdk/samtools/inttest.bam
delete mode 100644 src/test/resources/htsjdk/samtools/inttest.sam
delete mode 100644 src/test/resources/htsjdk/samtools/io/5newline5.txt
delete mode 100644 src/test/resources/htsjdk/samtools/io/slurptest.txt
delete mode 100644 src/test/resources/htsjdk/samtools/issue76.bam
delete mode 100644 src/test/resources/htsjdk/samtools/issue76.bam.bai
delete mode 100644 src/test/resources/htsjdk/samtools/liftover/hg18ToHg19.over.chain
delete mode 100644 src/test/resources/htsjdk/samtools/metrics/metricsOne.metrics
delete mode 100644 src/test/resources/htsjdk/samtools/metrics/metricsOneCopy.metrics
delete mode 100644 src/test/resources/htsjdk/samtools/metrics/metricsOneModifiedHistogram.metrics
delete mode 100644 src/test/resources/htsjdk/samtools/metrics/metricsOneModifiedMetrics.metrics
delete mode 100755 src/test/resources/htsjdk/samtools/queryname_sorted.sam
delete mode 100644 src/test/resources/htsjdk/samtools/readWithBadRname.sam
delete mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.dict
delete mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.noindex.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/reference/reference_with_trailing_whitespace.dict
delete mode 100644 src/test/resources/htsjdk/samtools/reference/reference_with_trailing_whitespace.fasta
delete mode 100644 src/test/resources/htsjdk/samtools/reference/testing.fai
delete mode 100644 src/test/resources/htsjdk/samtools/roundtrip.sam
delete mode 100644 src/test/resources/htsjdk/samtools/samFilter01.js
delete mode 100644 src/test/resources/htsjdk/samtools/samFilter02.js
delete mode 100755 src/test/resources/htsjdk/samtools/seekablestream/megabyteZeros.dat
delete mode 100644 src/test/resources/htsjdk/samtools/seekablestream/seekTest.txt
delete mode 100755 src/test/resources/htsjdk/samtools/sequenceWithSpace.bam
delete mode 100755 src/test/resources/htsjdk/samtools/sequenceWithSpace.sam
delete mode 100644 src/test/resources/htsjdk/samtools/serialization_test.bam
delete mode 100644 src/test/resources/htsjdk/samtools/serialization_test.bam.bai
delete mode 100644 src/test/resources/htsjdk/samtools/serialization_test.sam
delete mode 100644 src/test/resources/htsjdk/samtools/sra/test_archive.sra
delete mode 100644 src/test/resources/htsjdk/samtools/uncompressed.sam
delete mode 100755 src/test/resources/htsjdk/samtools/unsorted.sam
delete mode 100644 src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/5k-30BB2AAXX.3.aligned.sam.fastq
delete mode 100644 src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/illumina-as-standard.bam
delete mode 100644 src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/s_1_sequence.txt
delete mode 100644 src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa-as-standard.bam
delete mode 100644 src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa_full_range_as_solexa.fastq
delete mode 100644 src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/unmapped.sam
delete mode 100644 src/test/resources/htsjdk/samtools/util/defective_bgzf.bam
delete mode 100644 src/test/resources/htsjdk/samtools/util/no_bgzf_terminator.bam
delete mode 100644 src/test/resources/htsjdk/samtools/util/whitespace_text_file.txt
delete mode 100644 src/test/resources/htsjdk/tribble/Tb.vcf.idx
delete mode 100644 src/test/resources/htsjdk/tribble/basicDbSNP.dbsnp
delete mode 100644 src/test/resources/htsjdk/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19.bed
delete mode 100644 src/test/resources/htsjdk/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19_fixed.bed
delete mode 100644 src/test/resources/htsjdk/tribble/bed/Unigene.sample.bed
delete mode 100644 src/test/resources/htsjdk/tribble/bed/disconcontigs.bed
delete mode 100644 src/test/resources/htsjdk/tribble/bed/unsorted.bed
delete mode 100644 src/test/resources/htsjdk/tribble/complexExample.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/fakeBed.bed
delete mode 100644 src/test/resources/htsjdk/tribble/fakeVCF.vcf.gz
delete mode 100644 src/test/resources/htsjdk/tribble/fakeVCF.vcf.gz.tbi
delete mode 100644 src/test/resources/htsjdk/tribble/gwas/smallp.gwas
delete mode 100644 src/test/resources/htsjdk/tribble/index/chrY_Y4_small.bed
delete mode 100644 src/test/resources/htsjdk/tribble/large.txt
delete mode 100644 src/test/resources/htsjdk/tribble/sites.bed
delete mode 100644 src/test/resources/htsjdk/tribble/soapsnp.txt
delete mode 100644 src/test/resources/htsjdk/tribble/split/test.bin.part1
delete mode 100644 src/test/resources/htsjdk/tribble/split/test.bin.part2
delete mode 100644 src/test/resources/htsjdk/tribble/split/test.bin.part3
delete mode 100644 src/test/resources/htsjdk/tribble/split/test.bin.split
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz.tbi
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/bigger.vcf.gz.tbi
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf.gz
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/trioDup.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz
delete mode 100644 src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz.tbi
delete mode 100644 src/test/resources/htsjdk/tribble/test with spaces.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/test.bed
delete mode 100644 src/test/resources/htsjdk/tribble/test.gff
delete mode 100644 src/test/resources/htsjdk/tribble/test.tabix.bed.gz
delete mode 100644 src/test/resources/htsjdk/tribble/test.tabix.bed.gz.tbi
delete mode 100644 src/test/resources/htsjdk/tribble/test.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/test.vcf.bgz
delete mode 100644 src/test/resources/htsjdk/tribble/test.vcf.gz
delete mode 100644 src/test/resources/htsjdk/tribble/testGeliText.txt
delete mode 100644 src/test/resources/htsjdk/tribble/testIntervalList.list
delete mode 100644 src/test/resources/htsjdk/tribble/trio.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/trio.vcf.idx
delete mode 100644 src/test/resources/htsjdk/tribble/trioDup.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/vcfexample.vcf
delete mode 100644 src/test/resources/htsjdk/tribble/vcfexample.vcf.gz
delete mode 100644 src/test/resources/htsjdk/tribble/vcfexample.vcf.gz.tbi
delete mode 100644 src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.gz
delete mode 100644 src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.hdr.gz
delete mode 100644 src/test/resources/htsjdk/variant/HiSeq.10000.vcf
delete mode 100644 src/test/resources/htsjdk/variant/ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf
delete mode 100644 src/test/resources/htsjdk/variant/VCF4HeaderTest.vcf
delete mode 100644 src/test/resources/htsjdk/variant/VQSR.mixedTest.recal
delete mode 100644 src/test/resources/htsjdk/variant/breakpoint.vcf
delete mode 100644 src/test/resources/htsjdk/variant/dbsnp_135.b37.1000.vcf
delete mode 100644 src/test/resources/htsjdk/variant/diagnosis_targets_testfile.vcf
delete mode 100755 src/test/resources/htsjdk/variant/ex2.bgzf.bcf.csi
delete mode 100644 src/test/resources/htsjdk/variant/ex2.vcf
delete mode 100644 src/test/resources/htsjdk/variant/serialization_test.bcf
delete mode 100644 src/test/resources/htsjdk/variant/serialization_test.bcf.idx
delete mode 100644 src/test/resources/htsjdk/variant/structuralvariants.vcf
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.dict
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.fasta
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.fasta.fai
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/ScreenSamReads.100.input.sam
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/empty.interval_list
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.dict
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.vcf
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.vcf.idx
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1_comp.interval_list
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test2_comp.interval_list
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test3_comp.interval_list
delete mode 100644 src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test4_comp.interval_list
delete mode 100644 src/test/resources/htsjdk/variant/variantFilter01.js
delete mode 100644 src/test/resources/htsjdk/variant/variantFilter02.js
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/s_1_1101.filter
delete mode 100755 src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/L001/s_1_1101.clocs
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl
delete mode 100755 src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/N.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam
delete mode 100644 src/test/resources/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam
delete mode 100644 src/test/resources/testng.xml
create mode 100644 test/Makefile
create mode 100644 test/align/Makefile
create mode 100644 test/align/indextest.cpp
create mode 100644 test/cc/Makefile
create mode 100644 test/cc/asm-test.cpp
create mode 100644 test/cipher/Makefile
create mode 100755 test/cipher/test.sh
create mode 100644 test/judy_test/Makefile
create mode 100644 test/judy_test/judytest.c
create mode 100644 test/junit-4.11.jar
create mode 100644 test/kapp/Makefile
create mode 100644 test/kapp/env-test-tool.c
create mode 100644 test/kapp/kapp-test.cpp
create mode 100644 test/kapp/qfiletest.c
create mode 100644 test/kapp/queuefile.data
create mode 100644 test/kapp/report-kns-agent.c
create mode 100755 test/kapp/run-kns-agent.sh
create mode 100755 test/kapp/run-sig-core.sh
create mode 100644 test/kapp/sig-core.c
create mode 100644 test/kdb/Makefile
create mode 100644 test/kdb/kdbtest.cpp
create mode 100644 test/kdb/remote_open_test.cpp
create mode 100644 test/kdb/root/sra/SRR000123.sra.cache
create mode 100644 test/kdb/rowsettest.cpp
create mode 100644 test/kdb/test-btree.c
rename src/test/resources/htsjdk/samtools/cram/xx#blank.sam => test/kdb/testdb/tbl/SEQUENCE/col/dummy (100%)
create mode 100644 test/kdb/wkdbtest.cpp
create mode 100644 test/kfc/Makefile
create mode 100644 test/kfc/kfc.c
create mode 100644 test/kfc/test-except.c
create mode 100644 test/kfg/Makefile
create mode 100644 test/kfg/config.linux.kfg
create mode 100644 test/kfg/config.schema.kfg
create mode 100644 test/kfg/config.sra.kfg
create mode 100644 test/kfg/flat-sra-kfg.cpp
create mode 100644 test/kfg/flat-sra-kfg/aux_root/empty.kfg
create mode 100644 test/kfg/flat-sra-kfg/new/sraFlat.kfg
create mode 100644 test/kfg/flat-sra-kfg/old/fuse1000.kfg
create mode 100644 test/kfg/keystoretest.cpp
create mode 100644 test/kfg/kfgtest.cpp
create mode 100644 test/kfg/ncbi-home-from-env.configs/dir1/file.kfg
create mode 100644 test/kfg/ncbi-home-from-env.configs/dir1/not-user-settings.xml
create mode 100644 test/kfg/ncbi-home-from-env.configs/dir1/user-settings.mkfg
create mode 100644 test/kfg/ncbi-home-from-env.configs/dir2/file.kfg
create mode 100644 test/kfg/ncbi-home-from-env.configs/dir2/not-user-settings.xml
create mode 100644 test/kfg/ncbi-home-from-env.configs/dir2/user-settings.mkfg
create mode 100644 test/kfg/ncbi-home-from-env.cpp
create mode 100644 test/kfg/prj_2956.ngc
create mode 100644 test/kfg/repositorytest.cpp
create mode 100644 test/kfg/wb-test-kfg.cpp
create mode 100644 test/kfs/Makefile
create mode 100644 test/kfs/cacheteetest.cpp
create mode 100644 test/kfs/kfstest.cpp
create mode 100644 test/kfs/md5test.cpp
create mode 100644 test/kfs/ramfiletest.cpp
create mode 100644 test/kfs/resolvetest.cpp
create mode 100644 test/kfs/test.tar
create mode 100644 test/klib/Makefile
create mode 100644 test/klib/asm-test.c
create mode 100644 test/klib/md5appendtest.c
create mode 100644 test/klib/printf-test.c
create mode 100644 test/klib/test-SraReleaseVersion.cpp
create mode 100644 test/klib/test-klib.cpp
create mode 100644 test/klib/test-log.cpp
create mode 100644 test/klib/test-out.cpp
create mode 100644 test/klib/test-vnamelist.cpp
create mode 100644 test/kns/KNSManagerSingletonTest.cpp
create mode 100644 test/kns/Makefile
create mode 100644 test/kns/TestProxy.hpp
create mode 100644 test/kns/http-client.c
create mode 100644 test/kns/http-test.c
create mode 100644 test/kns/http_dropconnection_test.cpp
create mode 100644 test/kns/httptest.cpp
create mode 100644 test/kns/knstest.cpp
create mode 100644 test/kns/nih_1_out.txt
create mode 100644 test/kns/test-proxy-with-env.cpp
create mode 100644 test/kns/test-proxy.cpp
create mode 100644 test/kns/test-proxy.h
create mode 100644 test/kns/test-proxy/2-path-no-env/config
create mode 100644 test/kns/test-proxy/2-path-no-env/expected
create mode 100644 test/kns/test-proxy/2-path-no-port-no-env/config
create mode 100644 test/kns/test-proxy/2-path-no-port-no-env/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/disabled.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/disabled.MULTIPLE_PROXIES/environment
rename src/test/resources/htsjdk/samtools/io/empty.txt => test/kns/test-proxy/MULTIPLE_PROXIES/disabled.MULTIPLE_PROXIES/expected (100%)
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/enabled.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/enabled.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/enabled.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-kfg.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-kfg.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-kfg.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-only.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-only.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-only.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/ignore.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/ignore.MULTIPLE_PROXIES/environment
rename src/test/resources/tribble/tmp/.gitignore => test/kns/test-proxy/MULTIPLE_PROXIES/ignore.MULTIPLE_PROXIES/expected (100%)
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/kfg-env.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/kfg-env.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/kfg-env.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-not-only.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-not-only.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-not-only.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-only.MILTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-only.MILTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-only.MILTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/all/config
create mode 100644 test/kns/test-proxy/all/environment
create mode 100644 test/kns/test-proxy/all/expected
create mode 100644 test/kns/test-proxy/comma-error/environment
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/kns/test-proxy/comma-error/expected (100%)
create mode 100644 test/kns/test-proxy/disabled/config
create mode 100644 test/kns/test-proxy/disabled/environment
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/kns/test-proxy/disabled/expected (100%)
create mode 100644 test/kns/test-proxy/enabled/config
create mode 100644 test/kns/test-proxy/enabled/environment
create mode 100644 test/kns/test-proxy/enabled/expected
create mode 100644 test/kns/test-proxy/env-kfg/config
create mode 100644 test/kns/test-proxy/env-kfg/environment
create mode 100644 test/kns/test-proxy/env-kfg/expected
create mode 100644 test/kns/test-proxy/env-only/config
create mode 100644 test/kns/test-proxy/env-only/environment
create mode 100644 test/kns/test-proxy/env-only/expected
create mode 100644 test/kns/test-proxy/error/config
create mode 100644 test/kns/test-proxy/error/environment
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/kns/test-proxy/error/expected (100%)
create mode 100644 test/kns/test-proxy/http_proxy/environment
create mode 100644 test/kns/test-proxy/http_proxy/expected
create mode 100644 test/kns/test-proxy/ignore/config
create mode 100644 test/kns/test-proxy/ignore/environment
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/kns/test-proxy/ignore/expected (100%)
create mode 100644 test/kns/test-proxy/kfg-env/config
create mode 100644 test/kns/test-proxy/kfg-env/environment
create mode 100644 test/kns/test-proxy/kfg-env/expected
create mode 100644 test/kns/test-proxy/kfg-only/config
create mode 100644 test/kns/test-proxy/kfg-only/environment
create mode 100644 test/kns/test-proxy/kfg-only/expected
create mode 100644 test/kns/test-proxy/no-env/config
create mode 100644 test/kns/test-proxy/no-env/expected
create mode 100644 test/kns/test-proxy/no-port-no-env/config
create mode 100644 test/kns/test-proxy/no-port-no-env/expected
create mode 100644 test/kns/test-proxy/proxy-not-only/config
create mode 100644 test/kns/test-proxy/proxy-not-only/environment
create mode 100644 test/kns/test-proxy/proxy-not-only/expected
create mode 100644 test/kns/test-proxy/proxy-only/config
create mode 100644 test/kns/test-proxy/proxy-only/environment
create mode 100644 test/kns/test-proxy/proxy-only/expected
create mode 100644 test/kproc/Makefile
create mode 100644 test/kproc/kproctest.cpp
create mode 100644 test/krypto/Makefile
create mode 100644 test/krypto/test-aes-ciphers.c
create mode 100644 test/krypto/test-cipher-speed.c
create mode 100644 test/krypto/test-cmn.cpp
create mode 100644 test/krypto/test-cmn.hpp
create mode 100644 test/krypto/test-csprng.c
create mode 100644 test/krypto/test-encdec.cpp
create mode 100644 test/krypto/test-krypto-slow.cpp
create mode 100644 test/krypto/test-modes.c
create mode 100644 test/krypto/test-reenc.cpp
create mode 100644 test/ktst/Makefile
create mode 100644 test/ktst/ktsttest.cpp
create mode 100644 test/loader/Makefile
create mode 100644 test/loader/loadertest.cpp
create mode 100644 test/loader/sequence-writer.c
create mode 100755 test/loader/sequencewriter.vschema
create mode 100644 test/ngs-c++/CSRA1PileupTest.cpp
create mode 100644 test/ngs-c++/CSRA1_ReadCollection_test.cpp
create mode 100644 test/ngs-c++/CSRA1test.cpp
create mode 100644 test/ngs-c++/Makefile
create mode 100644 test/ngs-c++/NGStest.cpp
create mode 100644 test/ngs-c++/SRADBtest.cpp
create mode 100644 test/ngs-c++/SRAtest.cpp
create mode 100644 test/ngs-c++/SRR600096
create mode 100644 test/ngs-c++/SRR611340
create mode 100644 test/ngs-c++/ngsfixture.hpp
create mode 100644 test/ngs-c++/seq_spot_id_0.sra
create mode 100644 test/ngs-c++/valgrind.suppress
create mode 100644 test/ngs-java/Makefile
create mode 100644 test/ngs-java/build.xml
create mode 100644 test/ngs-java/ngs_test_CSRA1.java
create mode 100644 test/ngs-java/ngs_test_lib_load.java
create mode 100644 test/ngs-python/Makefile
create mode 100644 test/ngs-python/build.xml
create mode 100644 test/ngs-python/tests.py
create mode 100644 test/ngs/Makefile
create mode 100644 test/ngs/data/.gitignore
create mode 100644 test/ngs/data/SysPathTest/md/cur
create mode 100644 test/ngs/data/SysPathTest/md5
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/data
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/idx
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/idx0 (100%)
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/idx1
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/idx2
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/md/cur
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/col/READ/md5
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/md/cur
create mode 100644 test/ngs/data/SysPathTest/tbl/SEQUENCE/md5
create mode 100644 test/ngs/ngs_c_fixture.hpp
create mode 100644 test/ngs/ngstest.cpp
create mode 100644 test/ngs/ngstest_csra1.cpp
create mode 100644 test/ngs/ngstest_csra1_pileup.cpp
create mode 100644 test/ngs/ngstest_csra1_readcollection.cpp
create mode 100644 test/ngs/ngstest_csra1_refwin.cpp
create mode 100644 test/ngs/ngstest_fragmentblob.cpp
create mode 100644 test/ngs/ngstest_makedb.cpp
create mode 100644 test/ngs/ngstest_reference.cpp
create mode 100644 test/ngs/ngstest_sra.cpp
create mode 100644 test/ngs/ngstest_sradb.cpp
create mode 100644 test/ngs/valgrind.suppress
create mode 100644 test/only-remote-repository.kfg
create mode 100644 test/search/Makefile
create mode 100644 test/search/PerfCounter.h
create mode 100644 test/search/agrep-main.c
create mode 100644 test/search/search-vdb.cpp
create mode 100644 test/search/search-vdb.h
create mode 100644 test/search/test-agrep.cpp
create mode 100644 test/sraxf/Makefile
create mode 100644 test/sraxf/fix_read_seg-test.cpp
create mode 100644 test/vdb/.gitignore
create mode 100644 test/vdb/Makefile
create mode 100644 test/vdb/SYS-224064.cpp
create mode 100644 test/vdb/db/blob_val_inv_chsum.sra
create mode 100644 test/vdb/kfg/empty/empty.kfg
create mode 100644 test/vdb/kfg/linux/test-dependencies.kfg
create mode 100644 test/vdb/test-VDB-3060.cpp
create mode 100644 test/vdb/test-VDB-3061.cpp
create mode 100644 test/vdb/test-blob-val.cpp
create mode 100644 test/vdb/test-dependencies.cpp
create mode 100644 test/vdb/test-sparse-col.cpp
create mode 100644 test/vdb/test-vdb.cpp
create mode 100644 test/vdb/test-wvdb.cpp
create mode 100644 test/vfs/Makefile
create mode 100644 test/vfs/caching-kfg/incomplete.kfg
create mode 100644 test/vfs/managertest.cpp
create mode 100644 test/vfs/ncbi/protected1/SRR999997
create mode 100644 test/vfs/ncbi/protected1/SRR999997.ncbi_enc
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/ncbi/public/refseq/YYZZ99 (100%)
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/ncbi/public/refseq/ZZ999999.9 (100%)
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/ncbi/public/sra/SRR999998.sra (100%)
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/ncbi/public/wgs/YYZZ99 (100%)
create mode 100644 test/vfs/ncbi_enc
create mode 100644 test/vfs/path-test.c
create mode 100644 test/vfs/pathtest.cpp
create mode 100644 test/vfs/redirect-rejected-names-cgi-http-to-https.cpp
create mode 100644 test/vfs/redirect-rejected-names-cgi-http-to-https/incomplete.kfg
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/repo/wgs/WGS/YY/ZZ/YYZZ10 (100%)
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/repo/wgs/WGS/YY/ZZ/YYZZ99 (100%)
copy src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/repo/wgs2/WGS/YY/ZZ/YYZZ20 (100%)
rename src/main/java/htsjdk/tribble/util/ftp/.gitignore => test/vfs/repo/wgs2/WGS/YY/ZZ/YYZZ99 (100%)
create mode 100644 test/vfs/resolvertest.cpp
create mode 100644 test/vfs/test-caching.cpp
create mode 100644 test/vxf/Makefile
create mode 100644 test/vxf/VDB-2915.cpp
create mode 100644 test/vxf/local_config/local.kfg
create mode 100644 test/vxf/wb-irzip-impl.c
create mode 100644 test/vxf/wb-irzip-impl.h
create mode 100644 test/vxf/wb-test-vxf.cpp
create mode 100644 vdb3/itf/kfc/array.hpp
create mode 100644 vdb3/itf/kfc/atomic-ia32.hpp
create mode 100644 vdb3/itf/kfc/atomic-x86_64.hpp
create mode 100644 vdb3/itf/kfc/atomic.hpp
create mode 100644 vdb3/itf/kfc/callstk.hpp
create mode 100644 vdb3/itf/kfc/caps.hpp
create mode 100644 vdb3/itf/kfc/defs.hpp
create mode 100644 vdb3/itf/kfc/except.hpp
create mode 100644 vdb3/itf/kfc/fd.hpp
create mode 100644 vdb3/itf/kfc/fdmgr.hpp
create mode 100644 vdb3/itf/kfc/integer.hpp
create mode 100644 vdb3/itf/kfc/log.hpp
create mode 100644 vdb3/itf/kfc/memmgr.hpp
create mode 100644 vdb3/itf/kfc/memory.hpp
create mode 100644 vdb3/itf/kfc/ptr.hpp
create mode 100644 vdb3/itf/kfc/ref.hpp
create mode 100644 vdb3/itf/kfc/refcount.hpp
create mode 100644 vdb3/itf/kfc/rsrc.hpp
create mode 100644 vdb3/itf/kfc/stream.hpp
create mode 100644 vdb3/itf/kfc/string.hpp
create mode 100644 vdb3/itf/kfc/syserr.hpp
create mode 100644 vdb3/itf/kfc/task-impl.hpp
create mode 100644 vdb3/itf/kfc/task.hpp
create mode 100644 vdb3/itf/kfc/time.hpp
create mode 100644 vdb3/itf/kfc/timemgr.hpp
create mode 100644 vdb3/itf/kfc/vers.hpp
create mode 100644 vdb3/src/kfc/Makefile
create mode 100644 vdb3/src/kfc/array.cpp
create mode 100644 vdb3/src/kfc/callstk.cpp
create mode 100644 vdb3/src/kfc/except.cpp
create mode 100644 vdb3/src/kfc/fd.cpp
create mode 100644 vdb3/src/kfc/fdmgr.cpp
create mode 100644 vdb3/src/kfc/integer.cpp
create mode 100644 vdb3/src/kfc/log.cpp
create mode 100644 vdb3/src/kfc/memmgr.cpp
create mode 100644 vdb3/src/kfc/memory.cpp
create mode 100644 vdb3/src/kfc/pfdmgr.cpp
create mode 100644 vdb3/src/kfc/pfdmgr.hpp
create mode 100644 vdb3/src/kfc/plogger.cpp
create mode 100644 vdb3/src/kfc/plogger.hpp
create mode 100644 vdb3/src/kfc/pmemmgr.cpp
create mode 100644 vdb3/src/kfc/pmemmgr.hpp
create mode 100644 vdb3/src/kfc/ptimemgr.cpp
create mode 100644 vdb3/src/kfc/ptimemgr.hpp
create mode 100644 vdb3/src/kfc/ptr.cpp
create mode 100644 vdb3/src/kfc/ref.cpp
create mode 100644 vdb3/src/kfc/refcount.cpp
create mode 100644 vdb3/src/kfc/rsrc.cpp
create mode 100644 vdb3/src/kfc/stream.cpp
create mode 100644 vdb3/src/kfc/string.cpp
create mode 100644 vdb3/src/kfc/syserr.cpp
create mode 100644 vdb3/src/kfc/task-impl.cpp
create mode 100644 vdb3/src/kfc/task.cpp
create mode 100644 vdb3/src/kfc/time.cpp
create mode 100644 vdb3/src/kfc/timemgr.cpp
create mode 100644 vdb3/src/kfc/vers.cpp
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ncbi-vdb.git
More information about the debian-med-commit
mailing list