[med-svn] [infernal] 03/04: Merge tag 'upstream/1.1.2'
Sascha Steinbiss
satta at debian.org
Sat Aug 6 01:23:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository infernal.
commit e5b003eca3bf6507040cb27ffbbef2c1928b6867
Merge: 1fbf0cb b52cde2
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Aug 6 00:01:52 2016 +0000
Merge tag 'upstream/1.1.2'
Upstream version 1.1.2
COPYRIGHT | 46 -
INSTALL | 37 +-
LICENSE | 731 +-
Makefile.in | 25 +-
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RELEASE-NOTES | 192 +-
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hmmer/src/p7_hmmwindow.c | 34 +-
hmmer/src/p7_msvdata.c | 421 -
hmmer/src/p7_null3.c | 123 +-
hmmer/src/p7_pipeline.c | 906 +-
hmmer/src/p7_prior.c | 35 +-
hmmer/src/p7_profile.c | 8 +-
hmmer/src/p7_scoredata.c | 465 +
hmmer/src/p7_spensemble.c | 2 +-
hmmer/src/p7_tophits.c | 366 +-
hmmer/src/p7_trace.c | 6 +-
hmmer/src/phmmer.c | 358 +-
hmmer/src/seqmodel.c | 8 +-
hmmer/src/tracealign.c | 81 +-
hmmer/testsuite/2OG-FeII_Oxy_3-nt.hmm | 968 +
hmmer/testsuite/2OG-FeII_Oxy_3.hmm | 327 +
hmmer/testsuite/Makefile.in | 8 +-
hmmer/testsuite/i10-duplicate-names.pl | 2 +-
hmmer/testsuite/i11-hmmalign-mapali.pl | 2 +-
hmmer/testsuite/i12-delete-corruption.pl | 2 +-
hmmer/testsuite/i13-msa-integrity.pl | 2 +-
hmmer/testsuite/i17-stdin.pl | 2 +-
hmmer/testsuite/i18-nhmmer-generic.pl | 48 +-
hmmer/testsuite/i20-fmindex-core.pl | 2 +-
hmmer/testsuite/i9-optional-annotation.pl | 2 +-
hmmer/testsuite/testsuite.sqc | 100 +-
hmmer/tutorial/MADE1.hmm | 265 +
hmmer/tutorial/MADE1.out | 118 +
hmmer/tutorial/MADE1.sto | 4021 ++
hmmer/tutorial/SNORD96.hmm | 313 -
hmmer/tutorial/SNORD96.out | 82 -
hmmer/tutorial/SNORD96.sto | 16 -
hmmer/tutorial/dna_target.fa | 42680 +++----------------
hmmer/tutorial/fn3.hmm | 177 +-
hmmer/tutorial/fn3.out | 38 +-
hmmer/tutorial/globins4.hmm | 303 +-
hmmer/tutorial/globins4.out | 7489 ++--
hmmer/tutorial/minifam.h3f | Bin 54780 -> 54792 bytes
hmmer/tutorial/minifam.h3m | Bin 96927 -> 96927 bytes
hmmer/tutorial/minifam.h3p | Bin 113252 -> 113765 bytes
rmark/Makefile.in | 4 +-
rmark/rmark-create.c | 186 +-
src/Makefile.in | 4 +-
src/Rfam.12.1.claninfo | 104 +
src/alphabet.c | 2 +-
src/bandcyk-montecarlo-test.c | 6 +-
src/bandcyk-truncation-test.c | 9 +-
src/cm.c | 36 +-
src/cm_alidisplay.c | 6 +-
src/cm_alndata.c | 2 +-
src/cm_dispatch.h | 4 +-
src/cm_dpalign.c | 23 +-
src/cm_dpalign_trunc.c | 12 +-
src/cm_dpsearch.c | 26 +-
src/cm_dpsearch_trunc.c | 16 +-
src/cm_dpsmall.c | 6 +-
src/cm_file.c | 16 +-
src/cm_modelconfig.c | 6 +-
src/cm_modelmaker.c | 12 +-
src/cm_mx.c | 60 +-
src/cm_p7_modelmaker.c | 7 +-
src/cm_parsetree.c | 7 +-
src/cm_pipeline.c | 681 +-
src/cm_qdband.c | 6 +-
src/cm_submodel.c | 14 +-
src/cm_tophits.c | 1537 +-
src/cm_trunc.c | 2 +-
src/cmalign.c | 103 +-
src/cmbuild.c | 46 +-
src/cmcalibrate.c | 35 +-
src/cmconvert.c | 4 +-
src/cmemit.c | 8 +-
src/cmfetch.c | 4 +-
src/cmpress.c | 4 +-
src/cmscan.c | 1572 +-
src/cmsearch.c | 257 +-
src/cmstat.c | 4 +-
src/config.h.in | 2 +-
src/cp9-test.c | 4 +-
src/cp9.c | 4 +-
src/cp9_dp.c | 4 +-
src/cp9_modelmaker.c | 9 +-
src/cp9_trace.c | 10 +-
src/display.c | 6 +-
src/eweight.c | 6 +-
src/hmmband.c | 23 +-
src/hmmband.h | 4 +-
src/impl_sse/Makefile.in | 4 +-
src/impl_sse/impl_sse.h | 4 +-
src/impl_sse/sse_cm_dpsearch.c | 14 +-
src/impl_sse/sse_cm_dpsmall.c | 18 +-
src/impl_sse/sse_cmcons_hitmx.c | 6 +-
src/impl_sse/sse_cmcons_mscyk.c | 4 +-
src/infernal.h | 86 +-
src/mpisupport.c | 27 +-
src/prior.c | 2 +-
src/prior.h | 2 +-
src/sa-Makefile.in | 4 +-
src/sub_cm-test.c | 4 +-
src/trcyk.c | 2 -
testsuite/5.c.cm | 4815 +++
testsuite/5.claninfo | 1 +
testsuite/Makefile.in | 4 +-
testsuite/Rfam.12.1.clanin | 104 +
testsuite/bug-i1.pl | 2 +-
testsuite/bug-i38.pl | 2 +-
testsuite/bug-i44.pl | 82 +
testsuite/dev_testsuite.sqc | 23 +-
testsuite/emitted-5.fa | 19 +
testsuite/i1.pm | 81 +-
testsuite/itest2-duplicate-names.pl | 4 +-
testsuite/itest5-pipeline.pl | 8 +-
testsuite/itest6-sensitivity.pl | 16 +-
testsuite/itest7-trunc.pl | 24 +-
testsuite/itest8-glist.pl | 6 +-
testsuite/itest9-overlaps.pl | 174 +
testsuite/tRNA-Sec.c.cm | 701 +
testsuite/testsuite.sqc | 6 +
tutorial/tRNA5.c.cm | 14 +-
570 files changed, 60781 insertions(+), 64283 deletions(-)
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