[med-svn] [pirs] branch master updated (f7e5ab7 -> 5dd779b)
Andreas Tille
tille at debian.org
Tue Aug 9 09:53:47 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository pirs.
from f7e5ab7 Fix typo in link
new 1fe93f8 Newer version of pirs available at Github
new ed35311 Imported Upstream version 2.0.1+dfsg
new a187e55 Merge tag 'upstream/2.0.1+dfsg'
new ab60431 Try to build new upstream version
new 62806c1 Adjust to enable proper cleanup after build
new d195cf3 Imported Upstream version 2.0.1+dfsg
new 3e60327 Merge tag 'upstream/2.0.1+dfsg'
new d0d15e5 Make sure autoconf will not create broken configure script
new 6e424bd Does not build with +pie
new 9ad4dff Sequence of the libs is important
new 8844e13 New locations of build results
new 3661ac5 location of files has changed
new 26bcbe1 No static build
new c466519 Re-add example date for gcContCvgBias
new 55a9932 Adapt test suite
new 5dd779b Fix profile location
The 16 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:
.gitignore | 35 +
AUTHORS | 3 +
COPYING | 370 +++-
COPYING.LIB | 504 ------
INSTALL | 6 +-
MIRROR | 38 +
Makefile | 60 +-
NEWS | 135 ++
Profiles | 2 +-
README | 734 +++++---
alignment_stator | 1 -
baseCalling_Matrix_analyzer | 1 -
baseCalling_Matrix_calculator | 1 -
baseCalling_Matrix_merger | 1 -
debian/changelog | 2 +-
debian/clean | 16 +-
debian/control | 2 +-
debian/copyright | 27 +-
debian/patches/adjust_profiles_path.patch | 178 --
debian/patches/series | 1 -
.../patches/use_debian_packaged_libgzstream.patch | 85 +-
debian/pirs-examples.install | 4 +-
debian/pirs-profiles.install | 2 +-
debian/pirs.install | 4 +-
debian/rules | 41 +-
debian/tests/pirs-test | 7 +-
debian/watch | 2 +-
gc_coverage_bias_plot | 1 -
getprofile.sh.example | 4 +-
indelstat_sam_bam | 1 -
pirs | 1 -
src/AUTHORS | 1 +
src/COPYING | 1 +
src/{pirs => }/ChangeLog | 0
src/INSTALL | 34 +
src/Makefile.am | 1 +
src/NEWS | 1 +
src/README | 1 +
src/cleansrc.lst | 102 ++
src/config.h.in | 40 +
src/configure.ac | 75 +
src/genauto.sh | 6 +
src/pirs/AUTHORS | 1 -
src/pirs/BaseCallingProfile.cpp | 441 +++++
src/pirs/BaseCallingProfile.h | 39 +
src/pirs/CCRspline.h | 103 ++
src/pirs/COPYING | 340 ----
src/pirs/GCBiasProfile.cpp | 104 ++
src/pirs/GCBiasProfile.h | 26 +
src/pirs/INSTALL | 13 -
src/pirs/IndelProfile.cpp | 193 ++
src/pirs/IndelProfile.h | 45 +
src/pirs/InputStream.cpp | 171 ++
src/pirs/InputStream.h | 72 +
src/pirs/Lock.h | 60 +
src/pirs/Makefile.am | 76 +-
src/pirs/MaskQvalsByEamss.cpp | 169 ++
src/pirs/{src => }/MaskQvalsByEamss.h | 37 +-
src/pirs/OutputStream.cpp | 231 +++
src/pirs/OutputStream.h | 98 +
src/pirs/Profile.cpp | 36 +
src/pirs/Profile.h | 32 +
src/pirs/Profiles | 1 -
.../Base-Calling_Profiles/HG00513.PE76.matrix.gz | Bin
.../Base-Calling_Profiles/HG00536.PE76.matrix.gz | Bin
.../Base-Calling_Profiles/HG00702.PE91.matrix.gz | Bin
.../Base-Calling_Profiles/humNew.PE100.matrix.gz | Bin
.../GC-depth_Profiles/humNew.gcdep_100.dat | 0
.../GC-depth_Profiles/humNew.gcdep_150.dat | 0
.../GC-depth_Profiles/humNew.gcdep_200.dat | 0
.../Profiles/InDel_Profiles/phixv2.InDel.matrix | 0
src/pirs/README | 1 +
src/pirs/Random.h | 149 ++
src/pirs/Read.h | 140 ++
src/pirs/SFMT-src-1.4/SFMT-common.h | 164 ++
src/pirs/SFMT-src-1.4/SFMT-params.h | 98 +
src/pirs/SFMT-src-1.4/SFMT-params19937.h | 50 +
src/pirs/SFMT-src-1.4/SFMT.c | 427 +++++
src/pirs/SFMT-src-1.4/SFMT.h | 295 +++
src/pirs/SharedQueue.h | 68 +
src/pirs/SimulationParameters.h | 68 +
src/pirs/configure.ac | 34 -
src/pirs/gccMakefile | 61 +
src/pirs/main.cpp | 88 +
src/pirs/mt19937-64.cpp | 130 ++
src/pirs/mt19937-64.h | 14 +
src/pirs/pirs.h | 14 +
src/pirs/pirs_diploid.cpp | 757 ++++++++
src/pirs/pirs_simulate.cpp | 1874 ++++++++++++++++++++
src/pirs/src/Makefile.am | 11 -
src/pirs/src/MaskQvalsByEamss.cpp | 171 --
src/pirs/src/global.h | 30 -
src/pirs/src/load_file.cpp | 1126 ------------
src/pirs/src/load_file.h | 51 -
src/pirs/src/main.cpp | 51 -
src/pirs/src/simulate.cpp | 541 ------
src/pirs/src/simulate.h | 44 -
src/pirs/src/simulate_Illumina_reads.cpp | 1347 --------------
src/pirs/src/simulate_diploid_genome.cpp | 283 ---
src/pirs/src/test/pirs.sh | 4 -
src/pirs/test/pirs.sh | 7 +
src/pirs/{src => }/test/ref_seq.fa | 1 +
src/pirs/util.cpp | 327 ++++
src/pirs/util.h | 181 ++
src/srclean.sh | 12 +
src/stator/alignment_stator.pl | 4 +-
src/stator/baseCallingMatrix/autobam.pl | 2 +-
.../baseCalling_Matrix_analyzer.pl | 2 +-
...lator.pl => baseCalling_Matrix_calculator.0.pl} | 326 ++--
.../baseCalling_Matrix_calculator.pl | 391 ++--
.../baseCalling_Matrix_merger.old.pl | 186 ++
.../baseCallingMatrix/baseCalling_Matrix_merger.pl | 24 +-
src/stator/baseQualityTransition/gethist.pl | 19 +
src/stator/baseQualityTransition/hist.dem | 18 +
src/stator/baseQualityTransition/ifollowQ.pl | 148 ++
src/stator/baseQualityTransition/ifollowQmerge.pl | 156 ++
src/stator/baseQualityTransition/ifollowQplot.dem | 30 +
src/stator/baseQualityTransition/ifollowQplot.pl | 36 +
src/stator/baseQualityTransition/ifqQ.pl | 77 +
src/stator/baseQualityTransition/itilestator.pl | 94 +
src/stator/baseQualityTransition/pifollowQmerge.pl | 133 ++
src/stator/gcContCvgBias/AUTHORS | 1 -
src/stator/gcContCvgBias/COPYING | 340 ----
src/stator/gcContCvgBias/ChangeLog | 0
src/stator/gcContCvgBias/INSTALL | 13 -
src/stator/gcContCvgBias/Makefile | 50 +
src/stator/gcContCvgBias/Makefile.am | 6 -
src/stator/gcContCvgBias/NEWS | 2 -
src/stator/gcContCvgBias/README | 12 -
src/stator/gcContCvgBias/configure.ac | 29 -
.../{src => }/gc_coverage_bias_plot.pl | 2 +-
.../{src/test => }/gcdeptest.depth.gz | Bin
.../{src/test => }/gcdeptestref.fa.gz | Bin
src/stator/gcContCvgBias/loess.pl | 64 +
src/stator/gcContCvgBias/{src => }/main.cpp | 0
src/stator/gcContCvgBias/{src => }/self_util.cpp | 0
src/stator/gcContCvgBias/{src => }/self_util.h | 0
src/stator/gcContCvgBias/src/Makefile.am | 5 -
src/stator/gcContCvgBias/src/test/test.sh | 4 -
.../gcContCvgBias/{src => }/stat_soap_coverage.cpp | 7 +-
.../gcContCvgBias/{src => }/stat_soap_coverage.h | 0
src/stator/indel_hist.dem | 23 +
src/stator/indelstat_sam_bam.pl | 2 +-
143 files changed, 9647 insertions(+), 5997 deletions(-)
create mode 100644 .gitignore
create mode 100644 AUTHORS
delete mode 100644 COPYING.LIB
create mode 100644 MIRROR
delete mode 120000 alignment_stator
delete mode 120000 baseCalling_Matrix_analyzer
delete mode 120000 baseCalling_Matrix_calculator
delete mode 120000 baseCalling_Matrix_merger
delete mode 100644 debian/patches/adjust_profiles_path.patch
delete mode 120000 gc_coverage_bias_plot
delete mode 120000 indelstat_sam_bam
delete mode 120000 pirs
create mode 120000 src/AUTHORS
create mode 120000 src/COPYING
rename src/{pirs => }/ChangeLog (100%)
create mode 100644 src/INSTALL
create mode 100644 src/Makefile.am
create mode 120000 src/NEWS
create mode 120000 src/README
create mode 100644 src/cleansrc.lst
create mode 100644 src/config.h.in
create mode 100644 src/configure.ac
create mode 100755 src/genauto.sh
delete mode 100644 src/pirs/AUTHORS
create mode 100644 src/pirs/BaseCallingProfile.cpp
create mode 100644 src/pirs/BaseCallingProfile.h
create mode 100644 src/pirs/CCRspline.h
delete mode 100644 src/pirs/COPYING
create mode 100644 src/pirs/GCBiasProfile.cpp
create mode 100644 src/pirs/GCBiasProfile.h
delete mode 100644 src/pirs/INSTALL
create mode 100644 src/pirs/IndelProfile.cpp
create mode 100644 src/pirs/IndelProfile.h
create mode 100644 src/pirs/InputStream.cpp
create mode 100644 src/pirs/InputStream.h
create mode 100644 src/pirs/Lock.h
create mode 100644 src/pirs/MaskQvalsByEamss.cpp
rename src/pirs/{src => }/MaskQvalsByEamss.h (57%)
create mode 100644 src/pirs/OutputStream.cpp
create mode 100644 src/pirs/OutputStream.h
create mode 100644 src/pirs/Profile.cpp
create mode 100644 src/pirs/Profile.h
delete mode 120000 src/pirs/Profiles
rename src/pirs/{src => }/Profiles/Base-Calling_Profiles/HG00513.PE76.matrix.gz (100%)
rename src/pirs/{src => }/Profiles/Base-Calling_Profiles/HG00536.PE76.matrix.gz (100%)
rename src/pirs/{src => }/Profiles/Base-Calling_Profiles/HG00702.PE91.matrix.gz (100%)
rename src/pirs/{src => }/Profiles/Base-Calling_Profiles/humNew.PE100.matrix.gz (100%)
rename src/pirs/{src => }/Profiles/GC-depth_Profiles/humNew.gcdep_100.dat (100%)
rename src/pirs/{src => }/Profiles/GC-depth_Profiles/humNew.gcdep_150.dat (100%)
rename src/pirs/{src => }/Profiles/GC-depth_Profiles/humNew.gcdep_200.dat (100%)
rename src/pirs/{src => }/Profiles/InDel_Profiles/phixv2.InDel.matrix (100%)
create mode 120000 src/pirs/README
create mode 100644 src/pirs/Random.h
create mode 100644 src/pirs/Read.h
create mode 100644 src/pirs/SFMT-src-1.4/SFMT-common.h
create mode 100644 src/pirs/SFMT-src-1.4/SFMT-params.h
create mode 100644 src/pirs/SFMT-src-1.4/SFMT-params19937.h
create mode 100644 src/pirs/SFMT-src-1.4/SFMT.c
create mode 100644 src/pirs/SFMT-src-1.4/SFMT.h
create mode 100644 src/pirs/SharedQueue.h
create mode 100644 src/pirs/SimulationParameters.h
delete mode 100644 src/pirs/configure.ac
create mode 100644 src/pirs/gccMakefile
create mode 100644 src/pirs/main.cpp
create mode 100644 src/pirs/mt19937-64.cpp
create mode 100644 src/pirs/mt19937-64.h
create mode 100644 src/pirs/pirs.h
create mode 100644 src/pirs/pirs_diploid.cpp
create mode 100644 src/pirs/pirs_simulate.cpp
delete mode 100644 src/pirs/src/Makefile.am
delete mode 100644 src/pirs/src/MaskQvalsByEamss.cpp
delete mode 100644 src/pirs/src/global.h
delete mode 100644 src/pirs/src/load_file.cpp
delete mode 100644 src/pirs/src/load_file.h
delete mode 100644 src/pirs/src/main.cpp
delete mode 100644 src/pirs/src/simulate.cpp
delete mode 100644 src/pirs/src/simulate.h
delete mode 100644 src/pirs/src/simulate_Illumina_reads.cpp
delete mode 100644 src/pirs/src/simulate_diploid_genome.cpp
delete mode 100644 src/pirs/src/test/pirs.sh
create mode 100755 src/pirs/test/pirs.sh
rename src/pirs/{src => }/test/ref_seq.fa (99%)
create mode 100644 src/pirs/util.cpp
create mode 100644 src/pirs/util.h
create mode 100755 src/srclean.sh
copy src/stator/baseCallingMatrix/{baseCalling_Matrix_calculator.pl => baseCalling_Matrix_calculator.0.pl} (69%)
create mode 100755 src/stator/baseCallingMatrix/baseCalling_Matrix_merger.old.pl
create mode 100755 src/stator/baseQualityTransition/gethist.pl
create mode 100644 src/stator/baseQualityTransition/hist.dem
create mode 100755 src/stator/baseQualityTransition/ifollowQ.pl
create mode 100755 src/stator/baseQualityTransition/ifollowQmerge.pl
create mode 100644 src/stator/baseQualityTransition/ifollowQplot.dem
create mode 100755 src/stator/baseQualityTransition/ifollowQplot.pl
create mode 100644 src/stator/baseQualityTransition/ifqQ.pl
create mode 100755 src/stator/baseQualityTransition/itilestator.pl
create mode 100755 src/stator/baseQualityTransition/pifollowQmerge.pl
delete mode 100644 src/stator/gcContCvgBias/AUTHORS
delete mode 100644 src/stator/gcContCvgBias/COPYING
delete mode 100644 src/stator/gcContCvgBias/ChangeLog
delete mode 100644 src/stator/gcContCvgBias/INSTALL
create mode 100644 src/stator/gcContCvgBias/Makefile
delete mode 100644 src/stator/gcContCvgBias/Makefile.am
delete mode 100644 src/stator/gcContCvgBias/NEWS
delete mode 100644 src/stator/gcContCvgBias/README
delete mode 100644 src/stator/gcContCvgBias/configure.ac
rename src/stator/gcContCvgBias/{src => }/gc_coverage_bias_plot.pl (99%)
rename src/stator/gcContCvgBias/{src/test => }/gcdeptest.depth.gz (100%)
rename src/stator/gcContCvgBias/{src/test => }/gcdeptestref.fa.gz (100%)
create mode 100644 src/stator/gcContCvgBias/loess.pl
rename src/stator/gcContCvgBias/{src => }/main.cpp (100%)
rename src/stator/gcContCvgBias/{src => }/self_util.cpp (100%)
rename src/stator/gcContCvgBias/{src => }/self_util.h (100%)
delete mode 100644 src/stator/gcContCvgBias/src/Makefile.am
delete mode 100644 src/stator/gcContCvgBias/src/test/test.sh
rename src/stator/gcContCvgBias/{src => }/stat_soap_coverage.cpp (99%)
rename src/stator/gcContCvgBias/{src => }/stat_soap_coverage.h (100%)
create mode 100644 src/stator/indel_hist.dem
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