[med-svn] [libtfbs-perl] 03/08: Merge tag 'upstream/0.7.1'
Charles Plessy
plessy at moszumanska.debian.org
Sat Oct 21 02:48:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository libtfbs-perl.
commit 4eac69bc5f4dc247936c8de847d5a2388ec68b9e
Merge: 7ac36df 16bdbb0
Author: Charles Plessy <plessy at debian.org>
Date: Sat Oct 21 10:56:43 2017 +0900
Merge tag 'upstream/0.7.1'
Upstream version 0.7.1
# gpg: Signature faite le sam. 21 oct. 2017 10:56:39 JST
# gpg: avec la clef RSA 73471499CC60ED9EEE805946C5BD6C8F2295D502
# gpg: Bonne signature de « Charles Plessy <plessy at debian.org> » [totale]
# Empreinte de clef principale : 7347 1499 CC60 ED9E EE80 5946 C5BD 6C8F 2295 D502
Changes | 1 +
License | 2 +
MYMETA.json | 39 +
MYMETA.yml | 21 +
Makefile | 1161 ++++++++++++++++++++
Makefile.old | 1156 +++++++++++++++++++
README | 154 ---
README.md | 117 ++
TFBS/DB/JASPAR.pm | 8 +-
TFBS/DB/JASPAR2.pm | 2 +-
TFBS/DB/JASPAR4.pm | 4 +-
TFBS/DB/JASPAR5.pm | 2 +-
TFBS/DB/JASPAR6.pm | 2 +-
TFBS/DB/{JASPAR.pm => JASPAR7.pm} | 0
TFBS/DB/LocalTRANSFAC.pm | 2 +-
TFBS/DB/TRANSFAC.pm | 2 +-
TFBS/Matrix/Alignment.pm | 6 +-
TFBS/Matrix/ICM.pm | 2 +-
TFBS/Matrix/PWM.pm | 4 +-
TFBS/Matrix/_Alignment.pm | 2 +-
TFBS/MatrixSet.pm | 8 +-
TFBS/PatternGen.pm | 2 +-
TFBS/PatternGen/Elph.pm | 2 +-
TFBS/PatternGen/Gibbs.pm | 2 +-
TFBS/PatternGen/MEME.pm | 2 +-
TFBS/PatternGenI.pm | 2 +-
TFBS/Run/ConservationProfileGenerator.pm | 4 +-
TFBS/_Iterator/_MatrixSetIterator.pm | 54 +-
TFBS/_Iterator/_SiteSetIterator.pm | 14 +-
blib/arch/.exists | 0
blib/arch/auto/TFBS/.exists | 0
blib/arch/auto/TFBS/Ext/pwmsearch/.exists | 0
blib/arch/auto/TFBS/Ext/pwmsearch/pwmsearch.bs | 0
blib/arch/auto/TFBS/Ext/pwmsearch/pwmsearch.bundle | Bin 0 -> 50652 bytes
blib/bin/.exists | 0
blib/lib/.exists | 0
blib/lib/TFBS/DB.pm | 24 +
blib/lib/TFBS/DB/FlatFileDir.pm | 498 +++++++++
{TFBS => blib/lib/TFBS}/DB/JASPAR2.pm | 2 +-
{TFBS => blib/lib/TFBS}/DB/JASPAR4.pm | 10 +-
{TFBS => blib/lib/TFBS}/DB/LocalTRANSFAC.pm | 2 +-
{TFBS => blib/lib/TFBS}/DB/TRANSFAC.pm | 4 +-
blib/lib/TFBS/Ext/.exists | 0
blib/lib/TFBS/Ext/pwmsearch.pm | 161 +++
blib/lib/TFBS/Matrix.pm | 338 ++++++
{TFBS => blib/lib/TFBS}/Matrix/ICM.pm | 486 ++------
blib/lib/TFBS/Matrix/PFM.pm | 613 +++++++++++
{TFBS => blib/lib/TFBS}/Matrix/PWM.pm | 4 +-
{TFBS => blib/lib/TFBS}/Matrix/_Alignment.pm | 2 +-
{TFBS => blib/lib/TFBS}/MatrixSet.pm | 375 +------
{TFBS => blib/lib/TFBS}/PatternGen.pm | 4 +-
blib/lib/TFBS/PatternGen/AnnSpec.pm | 213 ++++
blib/lib/TFBS/PatternGen/AnnSpec/Motif.pm | 61 +
{TFBS => blib/lib/TFBS}/PatternGen/Elph.pm | 2 +-
blib/lib/TFBS/PatternGen/Elph/Motif.pm | 63 ++
{TFBS => blib/lib/TFBS}/PatternGen/Gibbs.pm | 2 +-
blib/lib/TFBS/PatternGen/Gibbs/Motif.pm | 102 ++
{TFBS => blib/lib/TFBS}/PatternGen/MEME.pm | 2 +-
blib/lib/TFBS/PatternGen/MEME/Motif.pm | 63 ++
blib/lib/TFBS/PatternGen/Motif/Matrix.pm | 50 +
blib/lib/TFBS/PatternGen/Motif/Word.pm | 21 +
blib/lib/TFBS/PatternGen/SimplePFM.pm | 125 +++
blib/lib/TFBS/PatternGen/YMF.pm | 193 ++++
blib/lib/TFBS/PatternGen/YMF/Motif.pm | 64 ++
{TFBS => blib/lib/TFBS}/PatternGenI.pm | 2 +-
blib/lib/TFBS/PatternI.pm | 163 +++
blib/lib/TFBS/Site.pm | 317 ++++++
blib/lib/TFBS/SitePair.pm | 80 ++
blib/lib/TFBS/SitePairSet.pm | 270 +++++
blib/lib/TFBS/SiteSet.pm | 266 +++++
blib/lib/TFBS/Tools/SetOperations.pm | 226 ++++
blib/lib/TFBS/Word.pm | 132 +++
blib/lib/TFBS/Word/Consensus.pm | 263 +++++
blib/lib/TFBS/_Iterator.pm | 71 ++
.../lib/TFBS}/_Iterator/_MatrixSetIterator.pm | 0
.../lib/TFBS}/_Iterator/_SiteSetIterator.pm | 0
blib/lib/auto/TFBS/.exists | 0
blib/lib/auto/TFBS/Ext/pwmsearch/.exists | 0
blib/lib/pwm_search.h | 129 +++
blib/lib/pwm_searchPFF.c | 785 +++++++++++++
blib/man1/.exists | 0
blib/man3/.exists | 0
blib/man3/TFBS::DB::FlatFileDir.3pm | 299 +++++
blib/man3/TFBS::DB::JASPAR2.3pm | 476 ++++++++
blib/man3/TFBS::DB::JASPAR4.3pm | 392 +++++++
blib/man3/TFBS::DB::LocalTRANSFAC.3pm | 221 ++++
blib/man3/TFBS::DB::TRANSFAC.3pm | 232 ++++
blib/man3/TFBS::Ext::pwmsearch.3pm | 155 +++
blib/man3/TFBS::Matrix.3pm | 214 ++++
blib/man3/TFBS::Matrix::ICM.3pm | 350 ++++++
blib/man3/TFBS::Matrix::PFM.3pm | 413 +++++++
blib/man3/TFBS::Matrix::PWM.3pm | 370 +++++++
blib/man3/TFBS::MatrixSet.3pm | 298 +++++
blib/man3/TFBS::PatternGen.3pm | 175 +++
blib/man3/TFBS::PatternGen::AnnSpec.3pm | 185 ++++
blib/man3/TFBS::PatternGen::AnnSpec::Motif.3pm | 153 +++
blib/man3/TFBS::PatternGen::Elph.3pm | 190 ++++
blib/man3/TFBS::PatternGen::Elph::Motif.3pm | 152 +++
blib/man3/TFBS::PatternGen::Gibbs.3pm | 191 ++++
blib/man3/TFBS::PatternGen::Gibbs::Motif.3pm | 169 +++
blib/man3/TFBS::PatternGen::MEME.3pm | 188 ++++
blib/man3/TFBS::PatternGen::MEME::Motif.3pm | 152 +++
blib/man3/TFBS::PatternGen::SimplePFM.3pm | 180 +++
blib/man3/TFBS::PatternGen::YMF.3pm | 188 ++++
blib/man3/TFBS::PatternGen::YMF::Motif.3pm | 152 +++
blib/man3/TFBS::PatternI.3pm | 206 ++++
blib/man3/TFBS::Site.3pm | 284 +++++
blib/man3/TFBS::SitePair.3pm | 162 +++
blib/man3/TFBS::SitePairSet.3pm | 241 ++++
blib/man3/TFBS::SiteSet.3pm | 232 ++++
blib/man3/TFBS::Word.3pm | 161 +++
blib/man3/TFBS::Word::Consensus.3pm | 233 ++++
blib/script/.exists | 0
pm_to_blib | 0
pod2htmd.tmp | 52 -
115 files changed, 14988 insertions(+), 1043 deletions(-)
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