[med-svn] [ncbi-vdb] 03/04: Merge tag 'upstream/2.8.1+dfsg'
Andreas Tille
tille at debian.org
Wed Jan 11 10:10:59 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ncbi-vdb.
commit fdd6a91ba3e20244232abe371bfa688684c0fb6e
Merge: bcf9fd2 879c0ec
Author: Andreas Tille <tille at debian.org>
Date: Wed Jan 11 07:18:09 2017 +0100
Merge tag 'upstream/2.8.1+dfsg'
Upstream version 2.8.1+dfsg
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configure | 45 +
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gradle/wrapper/gradle-wrapper.properties | 6 -
gradlew | 164 -
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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 +
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interfaces/cc/gcc/x86_64/byteswap.h | 89 +
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interfaces/cc/icc/compiler.h | 39 +
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interfaces/csra2/stats.vschema | 92 +
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interfaces/hdf5/kdf5.h | 89 +
interfaces/insdc/insdc.h | 277 +
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interfaces/insdc/seq.vschema | 210 +
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interfaces/kdb/btree.h | 188 +
interfaces/kdb/column.h | 360 +
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interfaces/kdb/database.h | 278 +
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interfaces/kdb/index.h | 309 +
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interfaces/kdb/meta.h | 411 +
interfaces/kdb/meta.hpp | 487 +
interfaces/kdb/namelist.h | 81 +
interfaces/kdb/rowset-impl.h | 141 +
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interfaces/loader/mmarray.h | 50 +
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interfaces/ngs/SimpleModel.graphml | 395 +
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interfaces/os/unix/oserror.h | 38 +
interfaces/os/unix/sysalloc.h | 40 +
interfaces/os/unix/unix-native.h | 58 +
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interfaces/search/extern.h | 41 +
interfaces/search/grep.h | 268 +
interfaces/search/nucstrstr.h | 153 +
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interfaces/search/smith-waterman.h | 72 +
interfaces/simple/extern.h | 41 +
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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 +
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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 +
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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 +
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libs/axf/cigar.c | 2578 ++
libs/axf/generate-mismatch-qual.c | 152 +
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libs/axf/get_mate_align_ids.c | 332 +
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libs/axf/mismatch-restore-qual.c | 135 +
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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 -
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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 +
3010 files changed, 635622 insertions(+), 299489 deletions(-)
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