Fri Apr 27 20:28:28 2018 UTC ()
biology/ncbi-blast+: import ncbi-blast+-2.7.1

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
between sequences. The program compares nucleotide or protein sequences to
sequence databases and calculates the statistical significance of matches.
BLAST can be used to infer functional and evolutionary relationships between
sequences as well as help identify members of gene families.

OK wiz@


(bacon)
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/DESCR
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/Makefile
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/PLIST
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/buildlink3.mk
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/distinfo
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
diff -r0 -r1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
File Added: pkgsrc/biology/ncbi-blast+/DESCR
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
between sequences. The program compares nucleotide or protein sequences to
sequence databases and calculates the statistical significance of matches.
BLAST can be used to infer functional and evolutionary relationships between
sequences as well as help identify members of gene families.
File Added: pkgsrc/biology/ncbi-blast+/Makefile
# $NetBSD: Makefile,v 1.1 2018/04/27 20:28:28 bacon Exp $

DISTNAME=	ncbi-blast-${PV}+-src
PKGNAME=	ncbi-blast+-${PV}
CATEGORIES=	biology
MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/

MAINTAINER=	bacon@NetBSD.org
HOMEPAGE=	http://blast.ncbi.nlm.nih.gov/
COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
LICENSE=	public-domain

# Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0
# Fix "unknown options" in configure
SUBST_CLASSES+=		configure
SUBST_STAGE.configure=	post-patch
SUBST_SED.configure+=	-e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
SUBST_SED.configure+=	-e '/--infodir=DIR/d'
SUBST_SED.configure+=	-e '/--mandir=DIR/d'
SUBST_FILES.configure+=	${WRKSRC}/src/build-system/configure

USE_TOOLS+=	gmake
USE_LANGUAGES=	c c++
GNU_CONFIGURE=	yes
# REPLACE_BASH=	compilers/xcode30_prj/configure
REPLACE_PERL=	src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
REPLACE_PYTHON=	src/app/winmasker/windowmasker_2.2.22_adapter.py

# The test for amq can hang, but amq is not needed so just avoid the test
# configure chooses /usr/local/bin/ar with no flags
# Resolve a conflict with libproj by moving libs to a subdir
CONFIGURE_ENV=		ncbi_cv_prog_amq_w=no
CONFIGURE_ARGS+=	AR="ar cr" --without-boost
CONFIGURE_ARGS+=	--libdir=${PREFIX}/lib/ncbi-tools++
# MAKE_JOBS_SAFE=		no	# Intermittent issues
WRKSRC=			${WRKDIR}/${DISTNAME}/c++

.include "../../mk/bsd.prefs.mk"

.if ${OPSYS} == NetBSD
# statfs is deprecated on NetBSD, but still exists in libc
# configure checks only for undefined reference, not for usability
CONFIGURE_ENV+=		ac_cv_func_statfs=no
.endif

PV=	2.7.1

post-install:
	${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
	${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so

.include "../../devel/zlib/buildlink3.mk"
.include "../../archivers/lzo/buildlink3.mk"
.include "../../archivers/bzip2/buildlink3.mk"
.include "../../devel/pcre/buildlink3.mk"
.include "../../databases/lmdb/buildlink3.mk"
.include "../../security/gnutls/buildlink3.mk"
.include "../../devel/gmp/buildlink3.mk"
.include "../../devel/libidn2/buildlink3.mk"
.include "../../security/nettle/buildlink3.mk"
.include "../../security/libtasn1/buildlink3.mk"
.include "../../security/p11-kit/buildlink3.mk"
.include "../../security/libgcrypt/buildlink3.mk"
.include "../../databases/sqlite3/buildlink3.mk"
.include "../../security/libgpg-error/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../mk/bsd.pkg.mk"
File Added: pkgsrc/biology/ncbi-blast+/PLIST
@comment $NetBSD: PLIST,v 1.1 2018/04/27 20:28:28 bacon Exp $
bin/blast_formatter
bin/blastdb_aliastool
bin/blastdbcheck
bin/blastdbcmd
bin/blastdbcp
bin/blastn
bin/blastp
bin/blastx
bin/convert2blastmask
bin/datatool
bin/deltablast
bin/dustmasker
bin/gc_cli
bin/gene_info_reader
bin/legacy_blast.pl
bin/makeblastdb
bin/makembindex
bin/makeprofiledb
bin/project_tree_builder
bin/psiblast
bin/rpsblast
bin/rpstblastn
bin/run_with_lock
bin/seedtop
bin/segmasker
bin/seqdb_demo
bin/seqdb_perf
bin/tblastn
bin/tblastx
bin/update_blastdb.pl
bin/windowmasker
bin/windowmasker_2.2.22_adapter.py
include/ncbi-tools++/algo/blast/api/bl2seq.hpp
include/ncbi-tools++/algo/blast/api/blast_advprot_options.hpp
include/ncbi-tools++/algo/blast/api/blast_aux.hpp
include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp
include/ncbi-tools++/algo/blast/api/blast_exception.hpp
include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp
include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp
include/ncbi-tools++/algo/blast/api/blast_options.hpp
include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp
include/ncbi-tools++/algo/blast/api/blast_options_handle.hpp
include/ncbi-tools++/algo/blast/api/blast_prot_options.hpp
include/ncbi-tools++/algo/blast/api/blast_results.hpp
include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
include/ncbi-tools++/algo/blast/api/blast_types.hpp
include/ncbi-tools++/algo/blast/api/blastp_kmer_options.hpp
include/ncbi-tools++/algo/blast/api/blastx_options.hpp
include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
include/ncbi-tools++/algo/blast/api/deltablast.hpp
include/ncbi-tools++/algo/blast/api/deltablast_options.hpp
include/ncbi-tools++/algo/blast/api/disc_nucl_options.hpp
include/ncbi-tools++/algo/blast/api/effsearchspace_calc.hpp
include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
include/ncbi-tools++/algo/blast/api/local_blast.hpp
include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
include/ncbi-tools++/algo/blast/api/local_search.hpp
include/ncbi-tools++/algo/blast/api/magicblast.hpp
include/ncbi-tools++/algo/blast/api/magicblast_options.hpp
include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
include/ncbi-tools++/algo/blast/api/phiblast_nucl_options.hpp
include/ncbi-tools++/algo/blast/api/phiblast_prot_options.hpp
include/ncbi-tools++/algo/blast/api/prelim_stage.hpp
include/ncbi-tools++/algo/blast/api/psi_pssm_input.hpp
include/ncbi-tools++/algo/blast/api/psibl2seq.hpp
include/ncbi-tools++/algo/blast/api/psiblast.hpp
include/ncbi-tools++/algo/blast/api/psiblast_iteration.hpp
include/ncbi-tools++/algo/blast/api/psiblast_options.hpp
include/ncbi-tools++/algo/blast/api/pssm_engine.hpp
include/ncbi-tools++/algo/blast/api/pssm_input.hpp
include/ncbi-tools++/algo/blast/api/query_data.hpp
include/ncbi-tools++/algo/blast/api/remote_blast.hpp
include/ncbi-tools++/algo/blast/api/remote_search.hpp
include/ncbi-tools++/algo/blast/api/repeats_filter.hpp
include/ncbi-tools++/algo/blast/api/rps_aux.hpp
include/ncbi-tools++/algo/blast/api/rpsblast_local.hpp
include/ncbi-tools++/algo/blast/api/rpstblastn_options.hpp
include/ncbi-tools++/algo/blast/api/search_strategy.hpp
include/ncbi-tools++/algo/blast/api/seedtop.hpp
include/ncbi-tools++/algo/blast/api/seqinfosrc_seqdb.hpp
include/ncbi-tools++/algo/blast/api/seqinfosrc_seqvec.hpp
include/ncbi-tools++/algo/blast/api/seqsrc_multiseq.hpp
include/ncbi-tools++/algo/blast/api/seqsrc_seqdb.hpp
include/ncbi-tools++/algo/blast/api/setup_factory.hpp
include/ncbi-tools++/algo/blast/api/sseqloc.hpp
include/ncbi-tools++/algo/blast/api/subj_ranges_set.hpp
include/ncbi-tools++/algo/blast/api/tblastn_options.hpp
include/ncbi-tools++/algo/blast/api/tblastx_options.hpp
include/ncbi-tools++/algo/blast/api/traceback_stage.hpp
include/ncbi-tools++/algo/blast/api/uniform_search.hpp
include/ncbi-tools++/algo/blast/api/version.hpp
include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
include/ncbi-tools++/algo/blast/blastinput/blast_asn1_input.hpp
include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
include/ncbi-tools++/algo/blast/blastinput/blast_scope_src.hpp
include/ncbi-tools++/algo/blast/blastinput/blastn_args.hpp
include/ncbi-tools++/algo/blast/blastinput/blastp_args.hpp
include/ncbi-tools++/algo/blast/blastinput/blastx_args.hpp
include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
include/ncbi-tools++/algo/blast/blastinput/kblastp_args.hpp
include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp
include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
include/ncbi-tools++/algo/blast/blastinput/rpstblastn_args.hpp
include/ncbi-tools++/algo/blast/blastinput/tblastn_args.hpp
include/ncbi-tools++/algo/blast/blastinput/tblastx_args.hpp
include/ncbi-tools++/algo/blast/composition_adjustment/compo_heap.h
include/ncbi-tools++/algo/blast/composition_adjustment/compo_mode_condition.h
include/ncbi-tools++/algo/blast/composition_adjustment/composition_adjustment.h
include/ncbi-tools++/algo/blast/composition_adjustment/composition_constants.h
include/ncbi-tools++/algo/blast/composition_adjustment/matrix_frequency_data.h
include/ncbi-tools++/algo/blast/composition_adjustment/nlm_linear_algebra.h
include/ncbi-tools++/algo/blast/composition_adjustment/optimize_target_freq.h
include/ncbi-tools++/algo/blast/composition_adjustment/redo_alignment.h
include/ncbi-tools++/algo/blast/composition_adjustment/smith_waterman.h
include/ncbi-tools++/algo/blast/composition_adjustment/unified_pvalues.h
include/ncbi-tools++/algo/blast/core/aa_ungapped.h
include/ncbi-tools++/algo/blast/core/blast_aalookup.h
include/ncbi-tools++/algo/blast/core/blast_aascan.h
include/ncbi-tools++/algo/blast/core/blast_def.h
include/ncbi-tools++/algo/blast/core/blast_diagnostics.h
include/ncbi-tools++/algo/blast/core/blast_encoding.h
include/ncbi-tools++/algo/blast/core/blast_engine.h
include/ncbi-tools++/algo/blast/core/blast_export.h
include/ncbi-tools++/algo/blast/core/blast_extend.h
include/ncbi-tools++/algo/blast/core/blast_filter.h
include/ncbi-tools++/algo/blast/core/blast_gapalign.h
include/ncbi-tools++/algo/blast/core/blast_hits.h
include/ncbi-tools++/algo/blast/core/blast_hspfilter.h
include/ncbi-tools++/algo/blast/core/blast_hspstream.h
include/ncbi-tools++/algo/blast/core/blast_kappa.h
include/ncbi-tools++/algo/blast/core/blast_lookup.h
include/ncbi-tools++/algo/blast/core/blast_message.h
include/ncbi-tools++/algo/blast/core/blast_nalookup.h
include/ncbi-tools++/algo/blast/core/blast_nascan.h
include/ncbi-tools++/algo/blast/core/blast_options.h
include/ncbi-tools++/algo/blast/core/blast_parameters.h
include/ncbi-tools++/algo/blast/core/blast_program.h
include/ncbi-tools++/algo/blast/core/blast_psi.h
include/ncbi-tools++/algo/blast/core/blast_query_info.h
include/ncbi-tools++/algo/blast/core/blast_rps.h
include/ncbi-tools++/algo/blast/core/blast_seg.h
include/ncbi-tools++/algo/blast/core/blast_seqsrc.h
include/ncbi-tools++/algo/blast/core/blast_seqsrc_impl.h
include/ncbi-tools++/algo/blast/core/blast_setup.h
include/ncbi-tools++/algo/blast/core/blast_stat.h
include/ncbi-tools++/algo/blast/core/blast_sw.h
include/ncbi-tools++/algo/blast/core/blast_toolkit.h
include/ncbi-tools++/algo/blast/core/blast_traceback.h
include/ncbi-tools++/algo/blast/core/blast_tune.h
include/ncbi-tools++/algo/blast/core/blast_util.h
include/ncbi-tools++/algo/blast/core/gapinfo.h
include/ncbi-tools++/algo/blast/core/gencode_singleton.h
include/ncbi-tools++/algo/blast/core/greedy_align.h
include/ncbi-tools++/algo/blast/core/hspfilter_besthit.h
include/ncbi-tools++/algo/blast/core/hspfilter_collector.h
include/ncbi-tools++/algo/blast/core/hspfilter_culling.h
include/ncbi-tools++/algo/blast/core/hspfilter_mapper.h
include/ncbi-tools++/algo/blast/core/link_hsps.h
include/ncbi-tools++/algo/blast/core/lookup_util.h
include/ncbi-tools++/algo/blast/core/lookup_wrap.h
include/ncbi-tools++/algo/blast/core/mb_indexed_lookup.h
include/ncbi-tools++/algo/blast/core/na_ungapped.h
include/ncbi-tools++/algo/blast/core/ncbi_math.h
include/ncbi-tools++/algo/blast/core/ncbi_std.h
include/ncbi-tools++/algo/blast/core/pattern.h
include/ncbi-tools++/algo/blast/core/phi_extend.h
include/ncbi-tools++/algo/blast/core/phi_gapalign.h
include/ncbi-tools++/algo/blast/core/phi_lookup.h
include/ncbi-tools++/algo/blast/core/spliced_hits.h
include/ncbi-tools++/algo/blast/core/split_query.h
include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
include/ncbi-tools++/algo/blast/format/blast_async_format.hpp
include/ncbi-tools++/algo/blast/format/blast_format.hpp
include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp
include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
include/ncbi-tools++/algo/blast/format/blastxml_format.hpp
include/ncbi-tools++/algo/blast/format/build_archive.hpp
include/ncbi-tools++/algo/blast/format/data4xml2format.hpp
include/ncbi-tools++/algo/blast/format/data4xmlformat.hpp
include/ncbi-tools++/algo/blast/format/sam.hpp
include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
include/ncbi-tools++/algo/blast/igblast/igblast.hpp
include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp
include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp
include/ncbi-tools++/algo/blast/proteinkmer/blastkmeroptions.hpp
include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp
include/ncbi-tools++/algo/blast/proteinkmer/blastkmerutils.hpp
include/ncbi-tools++/algo/blast/proteinkmer/kblastapi.hpp
include/ncbi-tools++/algo/blast/proteinkmer/mhfile.hpp
include/ncbi-tools++/algo/dustmask/sdust.tex
include/ncbi-tools++/algo/dustmask/symdust.hpp
include/ncbi-tools++/algo/segmask/segmask.hpp
include/ncbi-tools++/algo/winmask/README.API
include/ncbi-tools++/algo/winmask/seq_masker.hpp
include/ncbi-tools++/algo/winmask/seq_masker_cache_boost.hpp
include/ncbi-tools++/algo/winmask/seq_masker_istat.hpp
include/ncbi-tools++/algo/winmask/seq_masker_istat_ascii.hpp
include/ncbi-tools++/algo/winmask/seq_masker_istat_bin.hpp
include/ncbi-tools++/algo/winmask/seq_masker_istat_factory.hpp
include/ncbi-tools++/algo/winmask/seq_masker_istat_oascii.hpp
include/ncbi-tools++/algo/winmask/seq_masker_istat_obinary.hpp
include/ncbi-tools++/algo/winmask/seq_masker_ostat.hpp
include/ncbi-tools++/algo/winmask/seq_masker_ostat_ascii.hpp
include/ncbi-tools++/algo/winmask/seq_masker_ostat_bin.hpp
include/ncbi-tools++/algo/winmask/seq_masker_ostat_factory.hpp
include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt.hpp
include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_ascii.hpp
include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_bin.hpp
include/ncbi-tools++/algo/winmask/seq_masker_score.hpp
include/ncbi-tools++/algo/winmask/seq_masker_score_mean.hpp
include/ncbi-tools++/algo/winmask/seq_masker_score_mean_glob.hpp
include/ncbi-tools++/algo/winmask/seq_masker_score_min.hpp
include/ncbi-tools++/algo/winmask/seq_masker_uset_array.hpp
include/ncbi-tools++/algo/winmask/seq_masker_uset_hash.hpp
include/ncbi-tools++/algo/winmask/seq_masker_uset_simple.hpp
include/ncbi-tools++/algo/winmask/seq_masker_util.hpp
include/ncbi-tools++/algo/winmask/seq_masker_version.hpp
include/ncbi-tools++/algo/winmask/seq_masker_window.hpp
include/ncbi-tools++/algo/winmask/seq_masker_window_ambig.hpp
include/ncbi-tools++/algo/winmask/seq_masker_window_pattern.hpp
include/ncbi-tools++/algo/winmask/seq_masker_window_pattern_ambig.hpp
include/ncbi-tools++/algo/winmask/win_mask_config.hpp
include/ncbi-tools++/algo/winmask/win_mask_counts_converter.hpp
include/ncbi-tools++/algo/winmask/win_mask_dup_table.hpp
include/ncbi-tools++/algo/winmask/win_mask_gen_counts.hpp
include/ncbi-tools++/algo/winmask/win_mask_util.hpp
include/ncbi-tools++/cgi/caf.hpp
include/ncbi-tools++/cgi/cgi_exception.hpp
include/ncbi-tools++/cgi/cgi_serial.hpp
include/ncbi-tools++/cgi/cgi_session.hpp
include/ncbi-tools++/cgi/cgi_util.hpp
include/ncbi-tools++/cgi/cgiapp.hpp
include/ncbi-tools++/cgi/cgiapp_cached.hpp
include/ncbi-tools++/cgi/cgictx.hpp
include/ncbi-tools++/cgi/error_codes.hpp
include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
include/ncbi-tools++/cgi/ncbicgi.hpp
include/ncbi-tools++/cgi/ncbicgir.hpp
include/ncbi-tools++/cgi/ncbires.hpp
include/ncbi-tools++/cgi/ref_args.hpp
include/ncbi-tools++/cgi/user_agent.hpp
include/ncbi-tools++/common/boost_skew_guard.hpp
include/ncbi-tools++/common/config/ncbiconf_msvc.h
include/ncbi-tools++/common/config/ncbiconf_universal.h
include/ncbi-tools++/common/config/ncbiconf_xcode.h
include/ncbi-tools++/common/header_template.hpp
include/ncbi-tools++/common/metamodules_doxygen.h
include/ncbi-tools++/common/ncbi_build_ver.h
include/ncbi-tools++/common/ncbi_build_ver.h.in
include/ncbi-tools++/common/ncbi_build_ver.h.last
include/ncbi-tools++/common/ncbi_export.h
include/ncbi-tools++/common/ncbi_package_ver.h
include/ncbi-tools++/common/ncbi_pch_impl.hpp
include/ncbi-tools++/common/ncbi_skew_guard.h
include/ncbi-tools++/common/ncbi_source_ver.h
include/ncbi-tools++/common/ncbiconf_impl.h
include/ncbi-tools++/common/test_assert.h
include/ncbi-tools++/common/test_assert_impl.h
include/ncbi-tools++/common/test_data_path.h
include/ncbi-tools++/connect/connect_export.h
include/ncbi-tools++/connect/email_diag_handler.hpp
include/ncbi-tools++/connect/error_codes.hpp
include/ncbi-tools++/connect/impl/server_connection.hpp
include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
include/ncbi-tools++/connect/ncbi_base64.h
include/ncbi-tools++/connect/ncbi_buffer.h
include/ncbi-tools++/connect/ncbi_conn_exception.hpp
include/ncbi-tools++/connect/ncbi_conn_reader_writer.hpp
include/ncbi-tools++/connect/ncbi_conn_stream.hpp
include/ncbi-tools++/connect/ncbi_conn_test.hpp
include/ncbi-tools++/connect/ncbi_connection.h
include/ncbi-tools++/connect/ncbi_connector.h
include/ncbi-tools++/connect/ncbi_connutil.h
include/ncbi-tools++/connect/ncbi_core.h
include/ncbi-tools++/connect/ncbi_core_cxx.hpp
include/ncbi-tools++/connect/ncbi_file_connector.h
include/ncbi-tools++/connect/ncbi_ftp_connector.h
include/ncbi-tools++/connect/ncbi_gnutls.h
include/ncbi-tools++/connect/ncbi_heapmgr.h
include/ncbi-tools++/connect/ncbi_host_info.h
include/ncbi-tools++/connect/ncbi_http_connector.h
include/ncbi-tools++/connect/ncbi_http_session.hpp
include/ncbi-tools++/connect/ncbi_iprange.h
include/ncbi-tools++/connect/ncbi_ipv6.h
include/ncbi-tools++/connect/ncbi_lbos.hpp
include/ncbi-tools++/connect/ncbi_localip.h
include/ncbi-tools++/connect/ncbi_mbedtls.h
include/ncbi-tools++/connect/ncbi_memory_connector.h
include/ncbi-tools++/connect/ncbi_misc.hpp
include/ncbi-tools++/connect/ncbi_monkey.hpp
include/ncbi-tools++/connect/ncbi_namedpipe.hpp
include/ncbi-tools++/connect/ncbi_namedpipe_connector.hpp
include/ncbi-tools++/connect/ncbi_pipe.hpp
include/ncbi-tools++/connect/ncbi_pipe_connector.hpp
include/ncbi-tools++/connect/ncbi_sendmail.h
include/ncbi-tools++/connect/ncbi_server_info.h
include/ncbi-tools++/connect/ncbi_service.h
include/ncbi-tools++/connect/ncbi_service_connector.h
include/ncbi-tools++/connect/ncbi_socket.h
include/ncbi-tools++/connect/ncbi_socket.hpp
include/ncbi-tools++/connect/ncbi_socket_connector.h
include/ncbi-tools++/connect/ncbi_socket_unix.h
include/ncbi-tools++/connect/ncbi_socket_unix.hpp
include/ncbi-tools++/connect/ncbi_tls.h
include/ncbi-tools++/connect/ncbi_types.h
include/ncbi-tools++/connect/ncbi_userhost.hpp
include/ncbi-tools++/connect/ncbi_util.h
include/ncbi-tools++/connect/server.hpp
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include/ncbi-tools++/objtools/data_loaders/genbank/impl/processors.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id1_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_service.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/request_result.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/standalone_result.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/statistics.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader_interface.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader_params.h
include/ncbi-tools++/objtools/data_loaders/genbank/reader_service_params.h
include/ncbi-tools++/objtools/data_loaders/genbank/reader_snp.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/readers.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/readers/cache/reader_cache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/readers/cache/writer_cache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/readers/id1/reader_id1.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/readers/id2/reader_id2.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/readers/pubseqos/reader_pubseq.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/readers/pubseqos2/reader_pubseq2.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/seqref.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/writer.hpp
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include/ncbi-tools++/objtools/data_loaders/loaders.hpp
include/ncbi-tools++/objtools/edit/apply_object.hpp
include/ncbi-tools++/objtools/edit/autodef.hpp
include/ncbi-tools++/objtools/edit/autodef_options.hpp
include/ncbi-tools++/objtools/edit/autodef_source_desc.hpp
include/ncbi-tools++/objtools/edit/autodef_with_tax.hpp
include/ncbi-tools++/objtools/edit/capitalization_string.hpp
include/ncbi-tools++/objtools/edit/cds_fix.hpp
include/ncbi-tools++/objtools/edit/dblink_field.hpp
include/ncbi-tools++/objtools/edit/edit_exception.hpp
include/ncbi-tools++/objtools/edit/feattable_edit.hpp
include/ncbi-tools++/objtools/edit/field_handler.hpp
include/ncbi-tools++/objtools/edit/gap_trim.hpp
include/ncbi-tools++/objtools/edit/gaps_edit.hpp
include/ncbi-tools++/objtools/edit/gb_block_field.hpp
include/ncbi-tools++/objtools/edit/gene_utils.hpp
include/ncbi-tools++/objtools/edit/link_cds_mrna.hpp
include/ncbi-tools++/objtools/edit/loc_edit.hpp
include/ncbi-tools++/objtools/edit/mail_report.hpp
include/ncbi-tools++/objtools/edit/parse_text_options.hpp
include/ncbi-tools++/objtools/edit/promote.hpp
include/ncbi-tools++/objtools/edit/publication_edit.hpp
include/ncbi-tools++/objtools/edit/remote_updater.hpp
include/ncbi-tools++/objtools/edit/rna_edit.hpp
include/ncbi-tools++/objtools/edit/seq_entry_edit.hpp
include/ncbi-tools++/objtools/edit/seqid_guesser.hpp
include/ncbi-tools++/objtools/edit/source_edit.hpp
include/ncbi-tools++/objtools/edit/string_constraint.hpp
include/ncbi-tools++/objtools/edit/struc_comm_field.hpp
include/ncbi-tools++/objtools/edit/text_desc_field.hpp
include/ncbi-tools++/objtools/error_codes.hpp
include/ncbi-tools++/objtools/format/cigar_formatter.hpp
include/ncbi-tools++/objtools/format/context.hpp
include/ncbi-tools++/objtools/format/embl_formatter.hpp
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include/ncbi-tools++/objtools/format/feature_gather.hpp
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include/ncbi-tools++/objtools/format/flat_file_generator.hpp
include/ncbi-tools++/objtools/format/format_item_ostream.hpp
include/ncbi-tools++/objtools/format/formatter.hpp
include/ncbi-tools++/objtools/format/ftable_formatter.hpp
include/ncbi-tools++/objtools/format/ftable_gather.hpp
include/ncbi-tools++/objtools/format/gather_items.hpp
include/ncbi-tools++/objtools/format/gather_iter.hpp
include/ncbi-tools++/objtools/format/gbseq_formatter.hpp
include/ncbi-tools++/objtools/format/genbank_formatter.hpp
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include/ncbi-tools++/objtools/format/items/accession_item.hpp
include/ncbi-tools++/objtools/format/items/alignment_item.hpp
include/ncbi-tools++/objtools/format/items/basecount_item.hpp
include/ncbi-tools++/objtools/format/items/comment_item.hpp
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include/ncbi-tools++/objtools/format/items/ctrl_items.hpp
include/ncbi-tools++/objtools/format/items/date_item.hpp
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include/ncbi-tools++/objtools/format/items/defline_item.hpp
include/ncbi-tools++/objtools/format/items/feature_item.hpp
include/ncbi-tools++/objtools/format/items/flat_qual_slots.hpp
include/ncbi-tools++/objtools/format/items/flat_seqloc.hpp
include/ncbi-tools++/objtools/format/items/gap_item.hpp
include/ncbi-tools++/objtools/format/items/gene_finder.hpp
include/ncbi-tools++/objtools/format/items/genome_item.hpp
include/ncbi-tools++/objtools/format/items/genome_project_item.hpp
include/ncbi-tools++/objtools/format/items/html_anchor_item.hpp
include/ncbi-tools++/objtools/format/items/item.hpp
include/ncbi-tools++/objtools/format/items/item_base.hpp
include/ncbi-tools++/objtools/format/items/keywords_item.hpp
include/ncbi-tools++/objtools/format/items/locus_item.hpp
include/ncbi-tools++/objtools/format/items/origin_item.hpp
include/ncbi-tools++/objtools/format/items/primary_item.hpp
include/ncbi-tools++/objtools/format/items/qualifiers.hpp
include/ncbi-tools++/objtools/format/items/reference_item.hpp
include/ncbi-tools++/objtools/format/items/segment_item.hpp
include/ncbi-tools++/objtools/format/items/sequence_item.hpp
include/ncbi-tools++/objtools/format/items/source_item.hpp
include/ncbi-tools++/objtools/format/items/tsa_item.hpp
include/ncbi-tools++/objtools/format/items/version_item.hpp
include/ncbi-tools++/objtools/format/items/wgs_item.hpp
include/ncbi-tools++/objtools/format/ostream_text_ostream.hpp
include/ncbi-tools++/objtools/format/sam_formatter.hpp
include/ncbi-tools++/objtools/format/text_ostream.hpp
include/ncbi-tools++/objtools/readers/agp_converter.hpp
include/ncbi-tools++/objtools/readers/agp_read.hpp
include/ncbi-tools++/objtools/readers/agp_seq_entry.hpp
include/ncbi-tools++/objtools/readers/agp_util.hpp
include/ncbi-tools++/objtools/readers/agp_validate_reader.hpp
include/ncbi-tools++/objtools/readers/aln_reader.hpp
include/ncbi-tools++/objtools/readers/bed_reader.hpp
include/ncbi-tools++/objtools/readers/cigar.hpp
include/ncbi-tools++/objtools/readers/error_container.hpp
include/ncbi-tools++/objtools/readers/fasta.hpp
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include/ncbi-tools++/objtools/readers/format_guess_ex.hpp
include/ncbi-tools++/objtools/readers/getfeature.hpp
include/ncbi-tools++/objtools/readers/gff2_data.hpp
include/ncbi-tools++/objtools/readers/gff2_reader.hpp
include/ncbi-tools++/objtools/readers/gff3_reader.hpp
include/ncbi-tools++/objtools/readers/gff3_sofa.hpp
include/ncbi-tools++/objtools/readers/gff_reader.hpp
include/ncbi-tools++/objtools/readers/glimmer_reader.hpp
include/ncbi-tools++/objtools/readers/gtf_reader.hpp
include/ncbi-tools++/objtools/readers/gvf_reader.hpp
include/ncbi-tools++/objtools/readers/idmapper.hpp
include/ncbi-tools++/objtools/readers/iidmapper.hpp
include/ncbi-tools++/objtools/readers/line_error.hpp
include/ncbi-tools++/objtools/readers/message_listener.hpp
include/ncbi-tools++/objtools/readers/microarray_reader.hpp
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include/ncbi-tools++/objtools/readers/reader_base.hpp
include/ncbi-tools++/objtools/readers/reader_exception.hpp
include/ncbi-tools++/objtools/readers/reader_idgen.hpp
include/ncbi-tools++/objtools/readers/readfeat.hpp
include/ncbi-tools++/objtools/readers/rm_reader.hpp
include/ncbi-tools++/objtools/readers/source_mod_parser.hpp
include/ncbi-tools++/objtools/readers/source_mod_parser_wrapper.hpp
include/ncbi-tools++/objtools/readers/struct_cmt_reader.hpp
include/ncbi-tools++/objtools/readers/table_filter.hpp
include/ncbi-tools++/objtools/readers/track_data.hpp
include/ncbi-tools++/objtools/readers/ucscregion_reader.hpp
include/ncbi-tools++/objtools/readers/vcf_reader.hpp
include/ncbi-tools++/objtools/readers/wiggle_reader.hpp
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include/ncbi-tools++/objtools/seqmasks_io/mask_fasta_reader.hpp
include/ncbi-tools++/objtools/seqmasks_io/mask_reader.hpp
include/ncbi-tools++/objtools/seqmasks_io/mask_writer.hpp
include/ncbi-tools++/objtools/seqmasks_io/mask_writer_blastdb_maskinfo.hpp
include/ncbi-tools++/objtools/seqmasks_io/mask_writer_fasta.hpp
include/ncbi-tools++/objtools/seqmasks_io/mask_writer_int.hpp
include/ncbi-tools++/objtools/seqmasks_io/mask_writer_seqloc.hpp
include/ncbi-tools++/objtools/seqmasks_io/mask_writer_tab.hpp
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include/ncbi-tools++/serial/impl/objostr.inl
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include/ncbi-tools++/serial/impl/objstack.hpp
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lib/ncbi-tools++/libblastinput-static.a
lib/ncbi-tools++/libblastinput.a
lib/ncbi-tools++/libblastxml-static.a
lib/ncbi-tools++/libblastxml.a
lib/ncbi-tools++/libblastxml2-static.a
lib/ncbi-tools++/libblastxml2.a
lib/ncbi-tools++/libcdd-static.a
lib/ncbi-tools++/libcdd.a
lib/ncbi-tools++/libcn3d-static.a
lib/ncbi-tools++/libcn3d.a
lib/ncbi-tools++/libcomposition_adjustment-static.a
lib/ncbi-tools++/libcomposition_adjustment.a
lib/ncbi-tools++/libconnect-static.a
lib/ncbi-tools++/libconnect.a
lib/ncbi-tools++/libconnssl-static.a
lib/ncbi-tools++/libconnssl.a
lib/ncbi-tools++/libcreaders-static.a
lib/ncbi-tools++/libcreaders.a
lib/ncbi-tools++/libdbapi-static.a
lib/ncbi-tools++/libdbapi.a
lib/ncbi-tools++/libdbapi_driver-dll.so
lib/ncbi-tools++/libdbapi_driver-static.a
lib/ncbi-tools++/libdbapi_driver.a
lib/ncbi-tools++/libdocsum-static.a
lib/ncbi-tools++/libdocsum.a
lib/ncbi-tools++/libentrez2-static.a
lib/ncbi-tools++/libentrez2.a
lib/ncbi-tools++/libentrez2cli-static.a
lib/ncbi-tools++/libentrez2cli.a
lib/ncbi-tools++/libentrezgene-static.a
lib/ncbi-tools++/libentrezgene.a
lib/ncbi-tools++/libfeatdef-static.a
lib/ncbi-tools++/libfeatdef.a
lib/ncbi-tools++/libgbproj-static.a
lib/ncbi-tools++/libgbproj.a
lib/ncbi-tools++/libgbseq-static.a
lib/ncbi-tools++/libgbseq.a
lib/ncbi-tools++/libgencoll_client-static.a
lib/ncbi-tools++/libgencoll_client.a
lib/ncbi-tools++/libgene_info-static.a
lib/ncbi-tools++/libgene_info.a
lib/ncbi-tools++/libgeneral-static.a
lib/ncbi-tools++/libgeneral.a
lib/ncbi-tools++/libgenesbyloc-static.a
lib/ncbi-tools++/libgenesbyloc.a
lib/ncbi-tools++/libgenome_collection-static.a
lib/ncbi-tools++/libgenome_collection.a
lib/ncbi-tools++/libhomologene-static.a
lib/ncbi-tools++/libhomologene.a
lib/ncbi-tools++/libid1-static.a
lib/ncbi-tools++/libid1.a
lib/ncbi-tools++/libid1cli-static.a
lib/ncbi-tools++/libid1cli.a
lib/ncbi-tools++/libid2-static.a
lib/ncbi-tools++/libid2.a
lib/ncbi-tools++/libid2_split-static.a
lib/ncbi-tools++/libid2_split.a
lib/ncbi-tools++/libid2cli-static.a
lib/ncbi-tools++/libid2cli.a
lib/ncbi-tools++/libigblast-static.a
lib/ncbi-tools++/libigblast.a
lib/ncbi-tools++/libinsdseq-static.a
lib/ncbi-tools++/libinsdseq.a
lib/ncbi-tools++/libmacro-static.a
lib/ncbi-tools++/libmacro.a
lib/ncbi-tools++/libmedlars-static.a
lib/ncbi-tools++/libmedlars.a
lib/ncbi-tools++/libmedline-static.a
lib/ncbi-tools++/libmedline.a
lib/ncbi-tools++/libmim-static.a
lib/ncbi-tools++/libmim.a
lib/ncbi-tools++/libmla-static.a
lib/ncbi-tools++/libmla.a
lib/ncbi-tools++/libmlacli-static.a
lib/ncbi-tools++/libmlacli.a
lib/ncbi-tools++/libmmdb-static.a
lib/ncbi-tools++/libmmdb.a
lib/ncbi-tools++/libncbi_xblobstorage_netcache-static.a
lib/ncbi-tools++/libncbi_xblobstorage_netcache.a
lib/ncbi-tools++/libncbi_xcache_dbapi-dll.so
lib/ncbi-tools++/libncbi_xcache_dbapi-static.a
lib/ncbi-tools++/libncbi_xcache_dbapi.a
lib/ncbi-tools++/libncbi_xcache_netcache-dll.so
lib/ncbi-tools++/libncbi_xcache_netcache-static.a
lib/ncbi-tools++/libncbi_xcache_netcache.a
lib/ncbi-tools++/libncbi_xloader_blastdb-static.a
lib/ncbi-tools++/libncbi_xloader_blastdb.a
lib/ncbi-tools++/libncbi_xloader_blastdb_rmt-static.a
lib/ncbi-tools++/libncbi_xloader_blastdb_rmt.a
lib/ncbi-tools++/libncbi_xloader_genbank-dll.so
lib/ncbi-tools++/libncbi_xloader_genbank-static.a
lib/ncbi-tools++/libncbi_xloader_genbank.a
lib/ncbi-tools++/libncbi_xreader-dll.so
lib/ncbi-tools++/libncbi_xreader-static.a
lib/ncbi-tools++/libncbi_xreader.a
lib/ncbi-tools++/libncbi_xreader_cache-dll.so
lib/ncbi-tools++/libncbi_xreader_cache-static.a
lib/ncbi-tools++/libncbi_xreader_cache.a
lib/ncbi-tools++/libncbi_xreader_gicache-dll.so
lib/ncbi-tools++/libncbi_xreader_gicache-static.a
lib/ncbi-tools++/libncbi_xreader_gicache.a
lib/ncbi-tools++/libncbi_xreader_id1-dll.so
lib/ncbi-tools++/libncbi_xreader_id1-static.a
lib/ncbi-tools++/libncbi_xreader_id1.a
lib/ncbi-tools++/libncbi_xreader_id2-dll.so
lib/ncbi-tools++/libncbi_xreader_id2-static.a
lib/ncbi-tools++/libncbi_xreader_id2.a
lib/ncbi-tools++/libncbimime-static.a
lib/ncbi-tools++/libncbimime.a
lib/ncbi-tools++/libobjcoords-static.a
lib/ncbi-tools++/libobjcoords.a
lib/ncbi-tools++/libobjprt-static.a
lib/ncbi-tools++/libobjprt.a
lib/ncbi-tools++/libomssa-static.a
lib/ncbi-tools++/libomssa.a
lib/ncbi-tools++/libpcassay-static.a
lib/ncbi-tools++/libpcassay.a
lib/ncbi-tools++/libpcsubstance-static.a
lib/ncbi-tools++/libpcsubstance.a
lib/ncbi-tools++/libproj-static.a
lib/ncbi-tools++/libproj.a
lib/ncbi-tools++/libproteinkmer-static.a
lib/ncbi-tools++/libproteinkmer.a
lib/ncbi-tools++/libpub-static.a
lib/ncbi-tools++/libpub.a
lib/ncbi-tools++/libpubmed-static.a
lib/ncbi-tools++/libpubmed.a
lib/ncbi-tools++/libremap-static.a
lib/ncbi-tools++/libremap.a
lib/ncbi-tools++/libremapcli-static.a
lib/ncbi-tools++/libremapcli.a
lib/ncbi-tools++/libscoremat-static.a
lib/ncbi-tools++/libscoremat.a
lib/ncbi-tools++/libseq-static.a
lib/ncbi-tools++/libseq.a
lib/ncbi-tools++/libseqcode-static.a
lib/ncbi-tools++/libseqcode.a
lib/ncbi-tools++/libseqdb-static.a
lib/ncbi-tools++/libseqdb.a
lib/ncbi-tools++/libseqedit-static.a
lib/ncbi-tools++/libseqedit.a
lib/ncbi-tools++/libseqmasks_io-static.a
lib/ncbi-tools++/libseqmasks_io.a
lib/ncbi-tools++/libseqset-static.a
lib/ncbi-tools++/libseqset.a
lib/ncbi-tools++/libseqsplit-static.a
lib/ncbi-tools++/libseqsplit.a
lib/ncbi-tools++/libseqtest-static.a
lib/ncbi-tools++/libseqtest.a
lib/ncbi-tools++/libsequtil-static.a
lib/ncbi-tools++/libsequtil.a
lib/ncbi-tools++/libsqlitewrapp-static.a
lib/ncbi-tools++/libsqlitewrapp.a
lib/ncbi-tools++/libsubmit-static.a
lib/ncbi-tools++/libsubmit.a
lib/ncbi-tools++/libtables-static.a
lib/ncbi-tools++/libtables.a
lib/ncbi-tools++/libtaxon1-static.a
lib/ncbi-tools++/libtaxon1.a
lib/ncbi-tools++/libtaxon3-static.a
lib/ncbi-tools++/libtaxon3.a
lib/ncbi-tools++/libtest_mt-static.a
lib/ncbi-tools++/libtest_mt.a
lib/ncbi-tools++/libtinyseq-static.a
lib/ncbi-tools++/libtinyseq.a
lib/ncbi-tools++/libtrackmgr-static.a
lib/ncbi-tools++/libtrackmgr.a
lib/ncbi-tools++/libtrackmgrcli-static.a
lib/ncbi-tools++/libtrackmgrcli.a
lib/ncbi-tools++/libtrackmgrgridcli-static.a
lib/ncbi-tools++/libtrackmgrgridcli.a
lib/ncbi-tools++/libvalerr-static.a
lib/ncbi-tools++/libvalerr.a
lib/ncbi-tools++/libvalid-static.a
lib/ncbi-tools++/libvalid.a
lib/ncbi-tools++/libvariation-static.a
lib/ncbi-tools++/libvariation.a
lib/ncbi-tools++/libvarrep-static.a
lib/ncbi-tools++/libvarrep.a
lib/ncbi-tools++/libwritedb-static.a
lib/ncbi-tools++/libwritedb.a
lib/ncbi-tools++/libxalgoblastdbindex-static.a
lib/ncbi-tools++/libxalgoblastdbindex.a
lib/ncbi-tools++/libxalgodustmask-static.a
lib/ncbi-tools++/libxalgodustmask.a
lib/ncbi-tools++/libxalgosegmask-static.a
lib/ncbi-tools++/libxalgosegmask.a
lib/ncbi-tools++/libxalgowinmask-static.a
lib/ncbi-tools++/libxalgowinmask.a
lib/ncbi-tools++/libxalnmgr-static.a
lib/ncbi-tools++/libxalnmgr.a
lib/ncbi-tools++/libxblast-static.a
lib/ncbi-tools++/libxblast.a
lib/ncbi-tools++/libxblastformat-static.a
lib/ncbi-tools++/libxblastformat.a
lib/ncbi-tools++/libxcgi-static.a
lib/ncbi-tools++/libxcgi.a
lib/ncbi-tools++/libxcleanup-static.a
lib/ncbi-tools++/libxcleanup.a
lib/ncbi-tools++/libxcompress-static.a
lib/ncbi-tools++/libxcompress.a
lib/ncbi-tools++/libxconnect-static.a
lib/ncbi-tools++/libxconnect.a
lib/ncbi-tools++/libxconnserv-static.a
lib/ncbi-tools++/libxconnserv.a
lib/ncbi-tools++/libxcser-static.a
lib/ncbi-tools++/libxcser.a
lib/ncbi-tools++/libxfcgi-static.a
lib/ncbi-tools++/libxfcgi.a
lib/ncbi-tools++/libxformat-static.a
lib/ncbi-tools++/libxformat.a
lib/ncbi-tools++/libxhtml-static.a
lib/ncbi-tools++/libxhtml.a
lib/ncbi-tools++/libxncbi-static.a
lib/ncbi-tools++/libxncbi.a
lib/ncbi-tools++/libxnetblast-static.a
lib/ncbi-tools++/libxnetblast.a
lib/ncbi-tools++/libxnetblastcli-static.a
lib/ncbi-tools++/libxnetblastcli.a
lib/ncbi-tools++/libxobjedit-static.a
lib/ncbi-tools++/libxobjedit.a
lib/ncbi-tools++/libxobjmgr-static.a
lib/ncbi-tools++/libxobjmgr.a
lib/ncbi-tools++/libxobjread-static.a
lib/ncbi-tools++/libxobjread.a
lib/ncbi-tools++/libxobjreadex-static.a
lib/ncbi-tools++/libxobjreadex.a
lib/ncbi-tools++/libxobjsimple-static.a
lib/ncbi-tools++/libxobjsimple.a
lib/ncbi-tools++/libxobjutil-static.a
lib/ncbi-tools++/libxobjutil.a
lib/ncbi-tools++/libxregexp-static.a
lib/ncbi-tools++/libxregexp.a
lib/ncbi-tools++/libxregexp_template_tester-static.a
lib/ncbi-tools++/libxregexp_template_tester.a
lib/ncbi-tools++/libxser-static.a
lib/ncbi-tools++/libxser.a
lib/ncbi-tools++/libxthrserv-static.a
lib/ncbi-tools++/libxthrserv.a
lib/ncbi-tools++/libxutil-static.a
lib/ncbi-tools++/libxutil.a
lib/ncbi-tools++/libxxconnect-static.a
lib/ncbi-tools++/libxxconnect.a
File Added: pkgsrc/biology/ncbi-blast+/buildlink3.mk
# $NetBSD: buildlink3.mk,v 1.1 2018/04/27 20:28:28 bacon Exp $

BUILDLINK_TREE+=	ncbi-blast+

.if !defined(NCBI_BLAST+_BUILDLINK3_MK)
NCBI_BLAST+_BUILDLINK3_MK:=

BUILDLINK_API_DEPENDS.ncbi-blast++=	ncbi-blast+>=2.7.1
BUILDLINK_PKGSRCDIR.ncbi-blast+?=	../../wip/ncbi-blast+

.endif	# NCBI_BLAST+_BUILDLINK3_MK

BUILDLINK_TREE+=	-ncbi-blast+
File Added: pkgsrc/biology/ncbi-blast+/distinfo
$NetBSD: distinfo,v 1.1 2018/04/27 20:28:28 bacon Exp $

SHA1 (ncbi-blast-2.7.1+-src.tar.gz) = d04a25f01c386abd8515957a2ce1dabf376743f8
RMD160 (ncbi-blast-2.7.1+-src.tar.gz) = 7277419e16fb215aae4136a16e13bec963b70cbd
SHA512 (ncbi-blast-2.7.1+-src.tar.gz) = e4b3914f51165ae4c82051068ed9d3470687a4e0f1df6274018c0ba14b241666a570d72265c7d167b8ce2a9075652744244a00e3e95c00c4252da0fbd80d17c6
Size (ncbi-blast-2.7.1+-src.tar.gz) = 23254824 bytes
SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
SHA1 (patch-src_algo_blast_core_blast__kappa.c) = a580a5fb2d5a3af04c27dd63a7edd349b7ae1be7
SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97
SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6
SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = 0fb99ac4e582938fd47e66c146da71695f009b98
File Added: pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
$NetBSD: patch-compilers_xcode30__prj_configure,v 1.1 2018/04/27 20:28:28 bacon Exp $

# Nonportable extension

--- compilers/xcode30_prj/configure.orig	2018-04-27 14:19:43.000000000 +0000
+++ compilers/xcode30_prj/configure
@@ -280,7 +280,7 @@ arch=`arch`
 platform=`xcodebuild -version 2>/dev/null | grep 'Xcode [0-9][0-9]*' | sed -e 's/[ .]//g'`
 
 # ------- target architecture
-if test "$use_64" == "yes"; then
+if test "$use_64" = "yes"; then
   use_arch="x86_64"
 else
   use_arch="i386"
File Added: pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.1 2018/04/27 20:28:28 bacon Exp $

# Work around NetBSD stderr def choking macro

--- src/algo/blast/core/blast_kappa.c.orig	2018-03-26 21:55:44.000000000 +0000
+++ src/algo/blast/core/blast_kappa.c
@@ -32,6 +32,7 @@
  * system for each match in blastpgp
  */
 
+#include <stdio.h>
 #include <float.h>
 #include <algo/blast/core/ncbi_math.h>
 #include <algo/blast/core/blast_hits.h>
@@ -3404,13 +3405,15 @@ Blast_RedoAlignmentCore_MT(EBlastProgram
     }
 
     Boolean interrupt = FALSE;
+    /* NetBSD defines stderr as (&__sF[2]), which the macro below chokes on */
+    FILE *my_stderr = stderr;
 #pragma omp parallel \
     default(none) num_threads(actual_num_threads) \
     if(actual_num_threads>1) \
     shared(interrupt, seqsrc_tld, score_params_tld, hit_params_tld, \
     gap_align_tld, results_tld, \
     redoneMatches_tld, \
-    stderr, \
+    my_stderr, \
     numQueries, numMatches, theseMatches, \
     numFrames, program_number, subjectBlk_tld, positionBased, \
     default_db_genetic_code, localScalingFactor, queryInfo, \
File Added: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
$NetBSD: patch-src_build-system_Makefile.in.top,v 1.1 2018/04/27 20:28:28 bacon Exp $

# Add destdir suppot and fix perms on installed files

--- src/build-system/Makefile.in.top.orig	2017-02-01 16:52:02.000000000 +0000
+++ src/build-system/Makefile.in.top
@@ -37,22 +37,26 @@ check: $(PROJECTS)
 	fi
 
 install-toolkit:
-	-$(RMDIR) $(pincludedir)
-	$(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
-	$(INSTALL) $(lbindir)/* $(bindir)
-	$(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
+	-$(RMDIR) $(DESTDIR)$(pincludedir)
+	$(INSTALL) -d $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(pincludedir)
+	$(INSTALL) -m 755 $(lbindir)/* $(DESTDIR)$(bindir)
+	$(INSTALL) -m 644 $(llibdir)/*.* $(DESTDIR)$(libdir)
 	if test -d $(llibdir)/ncbi; then \
-	    cp -pPR $(llibdir)/ncbi $(libdir)/; \
+	    cp -pPR $(llibdir)/ncbi $(DESTDIR)$(libdir)/; \
 	fi
-	-rm -f $(libdir)/lib*-static.a
-	cd $(libdir)  && \
+	-rm -f $(DESTDIR)$(libdir)/lib*-static.a
+	cd $(DESTDIR)$(libdir)  && \
 	    for x in *.a; do \
 	        $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \
 	    done
+	find $(DESTDIR)$(libdir) -name '*.a' -exec chmod 644 '{}' \;
+	find $(DESTDIR)$(libdir) -name '*.so*' -exec chmod 755 '{}' \;
 	for d in $(includedir0) $(incdir); do \
 	    cd $$d && find * -name .svn -prune -o -print | \
-                cpio -pd $(pincludedir) ; \
+                cpio -pd $(DESTDIR)$(pincludedir) ; \
 	done
+	find $(DESTDIR)$(pincludedir) -type f -exec chmod 644 '{}' \;
+	find $(DESTDIR)$(pincludedir) -type d -exec chmod 755 '{}' \;
 ## set up appropriate build and status directories somewhere under $(libdir)?
 
 install-gbench:
File Added: pkgsrc/biology/ncbi-blast+/patches/Attic/patch-src_build-system_cmake_cmake-configure
$NetBSD: patch-src_build-system_cmake_cmake-configure,v 1.1 2018/04/27 20:28:28 bacon Exp $

# Fix portability issue

--- src/build-system/cmake/cmake-configure.orig	2018-03-26 14:13:44.229849356 +0000
+++ src/build-system/cmake/cmake-configure
@@ -468,7 +468,7 @@ fi
 if [ -z "$ROOT" ]; then
     if [ -z "$GPIPEROOT" ]; then
         ROOT="CMake-$BUILD_TYPE"
-        if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
+        if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
             ROOT="$ROOT"DLL
         fi
     else
File Added: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
$NetBSD: patch-src_build-system_configure,v 1.1 2018/04/27 20:28:28 bacon Exp $

# Fix support for localstatedir

--- src/build-system/configure.orig	2018-02-19 01:32:40 UTC
+++ src/build-system/configure
@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do
       | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
       | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
       | --datadir=* | --sysconfdir=* | --localstatedir=* \
-      | --with-runpath=* | --with-relative-runpath=* \
+      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
       | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
       | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
       | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
File Added: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.1 2018/04/27 20:28:28 bacon Exp $

# Missing RELRO for this one binary
# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=820959

--- src/build-system/helpers/Makefile.run_with_lock.app.orig	2018-04-27 16:21:07.000000000 +0000
+++ src/build-system/helpers/Makefile.run_with_lock.app
@@ -6,9 +6,9 @@ CC          = $(CC_FOR_BUILD)
 CC_WRAPPER  =
 CXX_WRAPPER =
 CPP         = $(CPP_FOR_BUILD)
-CFLAGS      = $(CFLAGS_FOR_BUILD)
-CPPFLAGS    = $(CPPFLAGS_FOR_BUILD)
-LDFLAGS     = $(LDFLAGS_FOR_BUILD)
+CFLAGS      = $(CFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now
+CPPFLAGS    = $(CPPFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now
+LDFLAGS     = $(LDFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now
 LIBS        = $(C_LIBS)
 LINK        = $(CC)
 LINK_WRAPPER =