[med-svn] [fasta3] 09/10: Update upstream source from tag 'upstream/36.3.8f'
Andreas Tille
tille at debian.org
Tue Dec 5 16:21:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fasta3.
commit c715d84a30fce24ffc7bb1535da52f1045358041
Merge: 9705b5b 2ee9899
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 5 17:20:11 2017 +0100
Update upstream source from tag 'upstream/36.3.8f'
Update to upstream version '36.3.8f'
with Debian dir 892509bae0e7d680ce21878b703289b7a3cfe5af
COPYRIGHT | 19 +
FASTA_LIST | 17 +
LICENSE | 202 ++
README | 77 +
README.md | 77 +
bin/README | 1 +
conf/README | 33 +
conf/fast_libs_e.www | 23 +
conf/fast_new | 38 +
conf/fastlibs | 42 +
data/VTML_10.mat | 35 +
data/VTML_120.mat | 34 +
data/VTML_160.mat | 34 +
data/VTML_20.mat | 34 +
data/VTML_200.mat | 34 +
data/VTML_40.mat | 34 +
data/VTML_80.mat | 34 +
data/blosum45.mat | 30 +
data/blosum50.mat | 29 +
data/blosum62.mat | 30 +
data/blosum80.mat | 30 +
data/dna.mat | 19 +
data/idn_aa.mat | 24 +
data/md_10.mat | 24 +
data/md_20.mat | 24 +
data/md_40.mat | 24 +
data/pam120.mat | 34 +
data/pam250.mat | 34 +
data/rna.mat | 19 +
data/vtml160.mat | 38 +
doc/INSTALL | 17 +
doc/README.versions | 48 +
doc/README_v36.3.8d.md | 37 +
doc/changes_v34.html | 351 +++
doc/changes_v35.html | 212 ++
doc/changes_v36.html | 467 ++++
doc/fasta.defaults | 17 +
doc/fasta.history.tex | 180 ++
doc/fasta.options | 55 +
doc/fasta36.1 | 467 ++++
doc/fasta_func.doc | 300 +++
doc/fasta_guide.bib | 265 +++
doc/fasta_guide.fg1.tex | 60 +
doc/fasta_guide.fg2.tex | 25 +
doc/fasta_guide.pdf | Bin 0 -> 265293 bytes
doc/fasta_guide.tex | 2115 ++++++++++++++++++
doc/fasta_versions.html | 101 +
doc/fastf3.1 | 176 ++
doc/fasts3.1 | 169 ++
doc/map_db.1 | 45 +
doc/prss3.1 | 170 ++
doc/ps_lav.1 | 20 +
doc/readme.v30 | 38 +
doc/readme.v30t6 | 74 +
doc/readme.v30t7 | 175 ++
doc/readme.v31t0 | 160 ++
doc/readme.v31t1 | 113 +
doc/readme.v32t0 | 407 ++++
doc/readme.v33t0 | 1268 +++++++++++
doc/readme.v34t0 | 1683 +++++++++++++++
doc/readme.v35 | 535 +++++
doc/readme.v36 | 2213 +++++++++++++++++++
doc/readme.w32 | 67 +
make/Makefile | 53 +
make/Makefile.NetBSD | 40 +
make/Makefile.cray_pvp | 41 +
make/Makefile.fcom | 344 +++
make/Makefile.freebsd | 72 +
make/Makefile.hpux_it | 56 +
make/Makefile.ibm | 37 +
make/Makefile.linux | 1 +
make/Makefile.linux32 | 63 +
make/Makefile.linux32_sse2 | 68 +
make/Makefile.linux64 | 1 +
make/Makefile.linux64_sse2 | 65 +
make/Makefile.linux_icc | 58 +
make/Makefile.linux_icc_sse2 | 55 +
make/Makefile.linux_mysql | 57 +
make/Makefile.linux_pgsql | 58 +
make/Makefile.linux_sql | 58 +
make/Makefile.linux_sse2 | 1 +
make/Makefile.mp_com2 | 116 +
make/Makefile.mpi_icc_sse2 | 55 +
make/Makefile.nm_fcom | 304 +++
make/Makefile.nm_pcom | 217 ++
make/Makefile.nmk_icl | 35 +
make/Makefile.os_x | 69 +
make/Makefile.os_x86 | 61 +
make/Makefile.os_x86_64 | 61 +
make/Makefile.os_x86_clang | 59 +
make/Makefile.os_x86_icc | 61 +
make/Makefile.pLinux | 83 +
make/Makefile.pLinux_sql | 81 +
make/Makefile.pcom | 229 ++
make/Makefile.pcom_s | 162 ++
make/Makefile.pcom_t | 184 ++
make/Makefile.sgi | 58 +
make/Makefile.sse_alt | 23 +
make/Makefile.sun | 52 +
make/Makefile.sun_x86 | 51 +
make/Makefile35.common | 45 +
make/Makefile35.common_sql | 50 +
make/Makefile35.nmk_com | 30 +
make/Makefile35m.common_mysql | 49 +
make/Makefile35m.common_pgsql | 49 +
make/Makefile35m.common_sql | 48 +
make/Makefile36.nmk_com | 30 +
make/Makefile36m.common | 51 +
make/Makefile36mpi.common | 43 +
make/Makefile36t.common | 43 +
make/README | 44 +
make/make_osx_univ.sh | 31 +
misc/README | 14 +
misc/parse_m9.pl | 139 ++
misc/res2R.pl | 22 +
misc/shuffle_embed.pl | 148 ++
psisearch2/README.md | 92 +
psisearch2/m89_btop_msa2.pl | 927 ++++++++
psisearch2/psisearch2_msa.pl | 453 ++++
psisearch2/psisearch2_msa.py | 368 ++++
scripts/README | 108 +
scripts/README.scripts | 84 +
scripts/acc_examples | 5 +
scripts/ann_exons_ens.pl | 287 +++
scripts/ann_exons_ncbi.pl | 243 +++
scripts/ann_exons_up_www.pl | 239 ++
scripts/ann_feats2ipr.pl | 526 +++++
scripts/ann_feats2ipr_e.pl | 544 +++++
scripts/ann_feats_up_sql.pl | 463 ++++
scripts/ann_feats_up_www2.pl | 455 ++++
scripts/ann_ipr_www.pl | 467 ++++
scripts/ann_pdb_cath.pl | 345 +++
scripts/ann_pdb_vast.pl | 320 +++
scripts/ann_pfam27.pl | 656 ++++++
scripts/ann_pfam28.pl | 782 +++++++
scripts/ann_pfam30.pl | 859 ++++++++
scripts/ann_pfam30_tmptbl.pl | 875 ++++++++
scripts/ann_pfam_www.pl | 687 ++++++
scripts/ann_script_list | 9 +
scripts/ann_upfeats_pfam_www_e.pl | 801 +++++++
scripts/annot_blast_btop2.pl | 1306 +++++++++++
scripts/blastp_cmd.sh | 31 +
scripts/color_defs.pl | 170 ++
scripts/exp_up_ensg.pl | 145 ++
scripts/expand_links.pl | 100 +
scripts/expand_uniref50.pl | 83 +
scripts/lav2plt.pl | 349 +++
scripts/lavplt_ps.pl | 540 +++++
scripts/lavplt_svg.pl | 461 ++++
scripts/links2sql.pl | 61 +
scripts/m8_btop_msa.pl | 412 ++++
scripts/m9B_btop_msa.pl | 654 ++++++
scripts/plot_domain2t.cgi | 667 ++++++
scripts/summ_domain_ident.pl | 97 +
scripts/test_ann_scripts.sh | 30 +
seq/bovgh.seq | 38 +
seq/bovprl.seq | 17 +
seq/dna_test_s.nlib | 47 +
seq/dyr_human.aa | 4 +
seq/egmsmg.aa | 19 +
seq/grou_drome.pseg | 14 +
seq/gst.nlib | 284 +++
seq/gst.seq | 20 +
seq/gstm1_human.vaa | 2 +
seq/gstm1b_human.nt | 17 +
seq/gstm1b_human_fs.nt | 17 +
seq/gstt1_drome.aa | 4 +
seq/gstt1_pssm.asn1 | Bin 0 -> 56931 bytes
seq/gtm1_human.aa | 4 +
seq/gtt1_drome.aa | 4 +
seq/h10_human.aa | 4 +
seq/hahu.aa | 4 +
seq/hsgstm1b.gcg | 214 ++
seq/hsgstm1b.seq | 40 +
seq/humgstd.seq | 20 +
seq/lcbo.aa | 5 +
seq/m1r.aa | 5 +
seq/m2.aa | 5 +
seq/mchu.aa | 3 +
seq/mgstm1.3nt | 60 +
seq/mgstm1.aa | 5 +
seq/mgstm1.aaa | 8 +
seq/mgstm1.e05 | 20 +
seq/mgstm1.eeq | 20 +
seq/mgstm1.esq | 20 +
seq/mgstm1.gcg | 13 +
seq/mgstm1.lc | 8 +
seq/mgstm1.nt | 12 +
seq/mgstm1.nt1 | 12 +
seq/mgstm1.nt12r | 26 +
seq/mgstm1.nt13 | 36 +
seq/mgstm1.nt13r | 35 +
seq/mgstm1.nt1r | 13 +
seq/mgstm1.nts | 9 +
seq/mgstm1.raa | 5 +
seq/mgstm1.rev | 16 +
seq/mgstm1.seq | 20 +
seq/mgstm1_genclone.seq | 2088 ++++++++++++++++++
seq/mgtt2_x.seq | 12 +
seq/ms1.aa | 6 +
seq/mu.lib | 50 +
seq/musplfm.aa | 9 +
seq/mwkw.aa | 31 +
seq/mwrtc1.aa | 8 +
seq/myosin_bp.aa | 20 +
seq/n0.aa | 4 +
seq/n1.aa | 5 +
seq/n2.aa | 28 +
seq/n2_fs.lib | 84 +
seq/n2s.aa | 8 +
seq/n2t.aa | 16 +
seq/n_fs.lib | 20 +
seq/ngt.aa | 20 +
seq/ngts.aa | 7 +
seq/oohu.aa | 6 +
seq/oohu.raa | 7 +
seq/prio_atepa.aa | 5 +
seq/prot_test.lib | 51 +
seq/prot_test.lseg | 66 +
seq/prot_test_s.lseg | 25 +
seq/qrhuld.aa | 15 +
seq/titin_hum.aa | 431 ++++
seq/titin_hum.seq | 1174 ++++++++++
seq/xurt8c.aa | 5 +
seq/xurt8c.lc | 5 +
seq/xurtg.aa | 5 +
sql/README | 26 +
sql/create_seq_demo.sql | 30 +
sql/join_up50.pl | 99 +
sql/mysql_demo1.sql | 6 +
sql/mysql_demo_pv.sql | 6 +
sql/nr_to_sql.pl | 103 +
sql/pirpsd.sql | 8 +
sql/psql_demo.sql | 7 +
sql/psql_demo1.sql | 6 +
sql/psql_demo_pv.sql | 7 +
src/a_mark.h | 51 +
src/aamap.h | 17 +
src/ag_stats.c | 129 ++
src/aln_structs.h | 61 +
src/alt_parms.h | 399 ++++
src/altlib.h | 142 ++
src/apam.c | 502 +++++
src/best_stats.h | 52 +
src/build_ares.c | 248 +++
src/c_dispn.c | 573 +++++
src/cal_cons.c | 1226 +++++++++++
src/cal_cons2.c | 1164 ++++++++++
src/cal_consf.c | 591 +++++
src/comp_lib9.c | 3052 ++++++++++++++++++++++++++
src/compacc2.c | 4119 +++++++++++++++++++++++++++++++++++
src/compacc2e.c | 4316 +++++++++++++++++++++++++++++++++++++
src/dec_pthr_subs.c | 246 +++
src/dec_pthr_subs.h | 42 +
src/defs.h | 171 ++
src/doinit.c | 975 +++++++++
src/drop_func.h | 185 ++
src/dropff2.c | 1394 ++++++++++++
src/dropfs2.c | 1681 +++++++++++++++
src/dropfx.c | 4072 ++++++++++++++++++++++++++++++++++
src/dropfx2.c | 3892 +++++++++++++++++++++++++++++++++
src/dropfz2.c | 3969 ++++++++++++++++++++++++++++++++++
src/dropfz3.c | 3864 +++++++++++++++++++++++++++++++++
src/dropgsw2.c | 1128 ++++++++++
src/dropgsw2.h | 46 +
src/dropnfa.c | 2250 +++++++++++++++++++
src/dropnfa.h | 84 +
src/dropnnw2.c | 900 ++++++++
src/dropnsw.c | 424 ++++
src/dyn_string.h | 30 +
src/faatran.c | 445 ++++
src/getenv.c | 56 +
src/getopt.c | 64 +
src/getseq.c | 313 +++
src/global_sse2.c | 547 +++++
src/global_sse2.h | 41 +
src/glocal_sse2.c | 596 +++++
src/glocal_sse2.h | 41 +
src/h_altlib.h | 28 +
src/htime.c | 43 +
src/initfa.c | 3183 +++++++++++++++++++++++++++
src/karlin.c | 519 +++++
src/last_tat.c | 155 ++
src/last_thresh.c | 62 +
src/lav_defs.h | 44 +
src/lib_sel.c | 341 +++
src/list_db.c | 245 +++
src/llgetaa.c | 497 +++++
src/lsim4.c | 998 +++++++++
src/lsim4.h | 145 ++
src/map_db.c | 600 ++++++
src/mm_file.h | 153 ++
src/mmgetaa.c | 1116 ++++++++++
src/mrandom.c | 97 +
src/msg.h | 57 +
src/mshowalign2.c | 999 +++++++++
src/mshowbest.c | 665 ++++++
src/mw.h | 49 +
src/mysql_lib.c | 636 ++++++
src/ncbl2_head.h | 35 +
src/ncbl2_mlib.c | 2442 +++++++++++++++++++++
src/ncbl_head.h | 33 +
src/ncbl_lib.c | 491 +++++
src/nmgetlib.c | 2254 +++++++++++++++++++
src/param.h | 251 +++
src/pcomp_bufs.h | 33 +
src/pcomp_subs2.c | 686 ++++++
src/pgsql_lib.c | 631 ++++++
src/print_pssm.c | 793 +++++++
src/pssm_asn_subs.c | 1756 +++++++++++++++
src/pthr_subs.h | 49 +
src/pthr_subs2.c | 377 ++++
src/randtest.c | 38 +
src/re_getlib.c | 146 ++
src/res_stats.c | 703 ++++++
src/rstruct.h | 16 +
src/sc_to_e.c | 71 +
src/scaleswn.c | 3136 +++++++++++++++++++++++++++
src/scaleswt.c | 1566 ++++++++++++++
src/showrss.c | 82 +
src/smith_waterman_altivec.c | 3086 ++++++++++++++++++++++++++
src/smith_waterman_altivec.h | 26 +
src/smith_waterman_sse2.c | 432 ++++
src/smith_waterman_sse2.h | 43 +
src/structs.h | 196 ++
src/tatstats.c | 583 +++++
src/tatstats.h | 160 ++
src/thr_buf_structs.h | 119 +
src/thr_bufs2.h | 41 +
src/uascii.h | 59 +
src/upam.h | 872 ++++++++
src/url_subs.c | 383 ++++
src/uthr_subs.h | 52 +
src/wm_align.c | 581 +++++
src/work_thr2.c | 492 +++++
test/results/README | 1 +
test/test.bat | 73 +
test/test.sh | 79 +
test/test2.sh | 53 +
test/test2G.sh | 79 +
test/test2V.sh | 28 +
test/test_mpi.pbs | 59 +
test/test_mpi1.pbs | 27 +
test/test_mpi2.pbs | 33 +
test/test_s.sh | 47 +
test/test_z.sh | 22 +
346 files changed, 116366 insertions(+)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasta3.git
More information about the debian-med-commit
mailing list