[med-svn] [libtfbs-perl] branch upstream updated (d61aae7 -> 16bdbb0)
Charles Plessy
plessy at moszumanska.debian.org
Sat Oct 21 02:48:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch upstream
in repository libtfbs-perl.
from d61aae7 Imported Upstream version 0.7.0+dfsg
new 16bdbb0 New upstream version 0.7.1
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
Changes | 1 +
License | 2 +
Ext/MYMETA.json => MYMETA.json | 4 +-
Ext/MYMETA.yml => MYMETA.yml | 4 +-
Ext/Makefile => Makefile | 704 +++++++++++++++------
Ext/Makefile.old => Makefile.old | 701 ++++++++++++++------
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 +-
Ext/pm_to_blib => blib/arch/.exists | 0
Ext/pm_to_blib => blib/arch/auto/TFBS/.exists | 0
.../arch/auto/TFBS/Ext/pwmsearch/.exists | 0
.../arch/auto/TFBS/Ext/pwmsearch}/pwmsearch.bs | 0
blib/arch/auto/TFBS/Ext/pwmsearch/pwmsearch.bundle | Bin 0 -> 50652 bytes
Ext/pm_to_blib => blib/bin/.exists | 0
Ext/pm_to_blib => blib/lib/.exists | 0
{TFBS => blib/lib/TFBS}/DB.pm | 0
{TFBS => blib/lib/TFBS}/DB/FlatFileDir.pm | 9 +-
{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 +-
Ext/pm_to_blib => blib/lib/TFBS/Ext/.exists | 0
{Ext => blib/lib/TFBS/Ext}/pwmsearch.pm | 0
{TFBS => blib/lib/TFBS}/Matrix.pm | 128 +---
{TFBS => blib/lib/TFBS}/Matrix/ICM.pm | 486 +++-----------
{TFBS => blib/lib/TFBS}/Matrix/PFM.pm | 0
{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 +-
{TFBS => blib/lib/TFBS}/PatternGen/AnnSpec.pm | 141 ++---
.../lib/TFBS}/PatternGen/AnnSpec/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Elph.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternGen/Elph/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Gibbs.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternGen/Gibbs/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/MEME.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternGen/MEME/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Motif/Matrix.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Motif/Word.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/SimplePFM.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/YMF.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/YMF/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGenI.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternI.pm | 0
{TFBS => blib/lib/TFBS}/Site.pm | 0
{TFBS => blib/lib/TFBS}/SitePair.pm | 13 +-
{TFBS => blib/lib/TFBS}/SitePairSet.pm | 0
{TFBS => blib/lib/TFBS}/SiteSet.pm | 0
{TFBS => blib/lib/TFBS}/Tools/SetOperations.pm | 0
{TFBS => blib/lib/TFBS}/Word.pm | 0
{TFBS => blib/lib/TFBS}/Word/Consensus.pm | 0
{TFBS => blib/lib/TFBS}/_Iterator.pm | 0
.../lib/TFBS}/_Iterator/_MatrixSetIterator.pm | 0
.../lib/TFBS}/_Iterator/_SiteSetIterator.pm | 0
Ext/pm_to_blib => blib/lib/auto/TFBS/.exists | 0
.../lib/auto/TFBS/Ext/pwmsearch/.exists | 0
{Ext => blib}/lib/pwm_search.h | 0
{Ext => blib}/lib/pwm_searchPFF.c | 0
Ext/pm_to_blib => blib/man1/.exists | 0
Ext/pm_to_blib => 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 +++++++
Ext/pm_to_blib => blib/script/.exists | 0
Ext/pm_to_blib => pm_to_blib | 0
pod2htmd.tmp | 52 --
115 files changed, 8426 insertions(+), 1641 deletions(-)
create mode 100644 License
copy Ext/MYMETA.json => MYMETA.json (93%)
copy Ext/MYMETA.yml => MYMETA.yml (91%)
copy Ext/Makefile => Makefile (52%)
copy Ext/Makefile.old => Makefile.old (53%)
delete mode 100644 README
create mode 100644 README.md
copy TFBS/DB/{JASPAR.pm => JASPAR7.pm} (100%)
copy Ext/pm_to_blib => blib/arch/.exists (100%)
copy Ext/pm_to_blib => blib/arch/auto/TFBS/.exists (100%)
copy Ext/pm_to_blib => blib/arch/auto/TFBS/Ext/pwmsearch/.exists (100%)
copy {Ext => blib/arch/auto/TFBS/Ext/pwmsearch}/pwmsearch.bs (100%)
create mode 100755 blib/arch/auto/TFBS/Ext/pwmsearch/pwmsearch.bundle
copy Ext/pm_to_blib => blib/bin/.exists (100%)
copy Ext/pm_to_blib => blib/lib/.exists (100%)
copy {TFBS => blib/lib/TFBS}/DB.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/FlatFileDir.pm (98%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/JASPAR2.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/JASPAR4.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/LocalTRANSFAC.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/TRANSFAC.pm (98%)
mode change 100755 => 100644
copy Ext/pm_to_blib => blib/lib/TFBS/Ext/.exists (100%)
copy {Ext => blib/lib/TFBS/Ext}/pwmsearch.pm (100%)
copy {TFBS => blib/lib/TFBS}/Matrix.pm (72%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/ICM.pm (59%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/PFM.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/PWM.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/_Alignment.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/MatrixSet.pm (59%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen.pm (97%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/AnnSpec.pm (63%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/AnnSpec/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Elph.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Elph/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Gibbs.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Gibbs/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/MEME.pm (98%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/MEME/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Motif/Matrix.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Motif/Word.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/SimplePFM.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/YMF.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/YMF/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGenI.pm (89%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternI.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Site.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/SitePair.pm (85%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/SitePairSet.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/SiteSet.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Tools/SetOperations.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Word.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Word/Consensus.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/_Iterator.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/_Iterator/_MatrixSetIterator.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/_Iterator/_SiteSetIterator.pm (100%)
mode change 100755 => 100644
copy Ext/pm_to_blib => blib/lib/auto/TFBS/.exists (100%)
copy Ext/pm_to_blib => blib/lib/auto/TFBS/Ext/pwmsearch/.exists (100%)
copy {Ext => blib}/lib/pwm_search.h (100%)
copy {Ext => blib}/lib/pwm_searchPFF.c (100%)
copy Ext/pm_to_blib => blib/man1/.exists (100%)
copy Ext/pm_to_blib => blib/man3/.exists (100%)
create mode 100644 blib/man3/TFBS::DB::FlatFileDir.3pm
create mode 100644 blib/man3/TFBS::DB::JASPAR2.3pm
create mode 100644 blib/man3/TFBS::DB::JASPAR4.3pm
create mode 100644 blib/man3/TFBS::DB::LocalTRANSFAC.3pm
create mode 100644 blib/man3/TFBS::DB::TRANSFAC.3pm
create mode 100644 blib/man3/TFBS::Ext::pwmsearch.3pm
create mode 100644 blib/man3/TFBS::Matrix.3pm
create mode 100644 blib/man3/TFBS::Matrix::ICM.3pm
create mode 100644 blib/man3/TFBS::Matrix::PFM.3pm
create mode 100644 blib/man3/TFBS::Matrix::PWM.3pm
create mode 100644 blib/man3/TFBS::MatrixSet.3pm
create mode 100644 blib/man3/TFBS::PatternGen.3pm
create mode 100644 blib/man3/TFBS::PatternGen::AnnSpec.3pm
create mode 100644 blib/man3/TFBS::PatternGen::AnnSpec::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Elph.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Elph::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Gibbs.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Gibbs::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::MEME.3pm
create mode 100644 blib/man3/TFBS::PatternGen::MEME::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::SimplePFM.3pm
create mode 100644 blib/man3/TFBS::PatternGen::YMF.3pm
create mode 100644 blib/man3/TFBS::PatternGen::YMF::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternI.3pm
create mode 100644 blib/man3/TFBS::Site.3pm
create mode 100644 blib/man3/TFBS::SitePair.3pm
create mode 100644 blib/man3/TFBS::SitePairSet.3pm
create mode 100644 blib/man3/TFBS::SiteSet.3pm
create mode 100644 blib/man3/TFBS::Word.3pm
create mode 100644 blib/man3/TFBS::Word::Consensus.3pm
copy Ext/pm_to_blib => blib/script/.exists (100%)
copy Ext/pm_to_blib => pm_to_blib (100%)
delete mode 100644 pod2htmd.tmp
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