From 10e319e02e85d638bd59696b6471db8152787950 Mon Sep 17 00:00:00 2001 From: Dat T Nguyen Date: Fri, 8 Jul 2022 12:13:06 +0200 Subject: [PATCH] v1.0.0 --- {Circall_v0.2.0 => Circall_v1.0.0}/.DS_Store | Bin .../Circall_source.sh | 0 .../Data/Circall_depdata_human.RData | Bin .../Data/test_read1.fasta.gz | Bin .../Data/test_read2.fasta.gz | Bin .../R/Circall_functions.R | 0 .../R/Circall_simulator.R | 0 {Circall_v0.2.0 => Circall_v1.0.0}/R/buildBSJdb.R | 0 {Circall_v0.2.0 => Circall_v1.0.0}/R/createSqlite.R | 0 .../R/doPairEndFiltering.R | 0 .../R/doSingleEndFiltering.R | 0 {Circall_v0.2.0 => Circall_v1.0.0}/R/export.R | 0 {Circall_v0.2.0 => Circall_v1.0.0}/R/getFdr.R | 0 .../R/getPseudoCircRNAsequence.R | 0 .../R/load_packages.R | 0 {Circall_v0.2.0 => Circall_v1.0.0}/config.sh | 0 .../include/EmpiricalDistribution.hpp | 0 .../include/EquivalenceClassBuilder.hpp | 0 .../include/ExportFeq.hpp | 0 .../include/ReadExperiment.hpp | 0 .../include/SACollectorCircall.hpp | 0 .../include/spdlog/details/format.h | 0 {Circall_v0.2.0 => Circall_v1.0.0}/install.sh | 0 {Circall_v0.2.0 => Circall_v1.0.0}/linux/.DS_Store | Bin .../linux/bin/Circall_bsj | Bin .../linux/bin/Circall_pseudo | Bin .../linux/bin/Circall_wt | Bin .../linux/bin/TxIndexer | Bin .../linux/bin/buildBSJdb.R | 0 .../linux/bin/createSqlite.R | 0 .../linux/lib/libgcc_s.so.1 | Bin .../linux/lib/libgomp.so.1 | Bin .../linux/lib/libm.so.6 | Bin .../linux/lib/libsailfish_core.a | Bin .../linux/lib/libtbb.so | 0 .../linux/lib/libtbb.so.2 | Bin .../linux/lib/libtbbmalloc.so | 0 .../linux/lib/libtbbmalloc.so.2 | Bin .../linux/lib/libtbbmalloc_proxy.so | 0 .../linux/lib/libtbbmalloc_proxy.so.2 | Bin .../src/CMakeLists.txt | 0 .../src/Circall_bsj.cpp | 0 .../src/Circall_pseudo.cpp | 0 .../src/Circall_wt.cpp | 0 .../src/EmpiricalDistribution.cpp | 0 .../src/ExportFeq.cpp | 0 .../src/TxIndexer.cpp | 0 Dockerfile | 2 +- 48 files changed, 1 insertion(+), 1 deletion(-) rename {Circall_v0.2.0 => Circall_v1.0.0}/.DS_Store (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/Circall_source.sh (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/Data/Circall_depdata_human.RData (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/Data/test_read1.fasta.gz (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/Data/test_read2.fasta.gz (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/Circall_functions.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/Circall_simulator.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/buildBSJdb.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/createSqlite.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/doPairEndFiltering.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/doSingleEndFiltering.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/export.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/getFdr.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/getPseudoCircRNAsequence.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/R/load_packages.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/config.sh (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/include/EmpiricalDistribution.hpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/include/EquivalenceClassBuilder.hpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/include/ExportFeq.hpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/include/ReadExperiment.hpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/include/SACollectorCircall.hpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/include/spdlog/details/format.h (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/install.sh (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/.DS_Store (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/bin/Circall_bsj (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/bin/Circall_pseudo (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/bin/Circall_wt (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/bin/TxIndexer (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/bin/buildBSJdb.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/bin/createSqlite.R (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libgcc_s.so.1 (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libgomp.so.1 (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libm.so.6 (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libsailfish_core.a (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libtbb.so (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libtbb.so.2 (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libtbbmalloc.so (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libtbbmalloc.so.2 (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libtbbmalloc_proxy.so (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/linux/lib/libtbbmalloc_proxy.so.2 (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/src/CMakeLists.txt (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/src/Circall_bsj.cpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/src/Circall_pseudo.cpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/src/Circall_wt.cpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/src/EmpiricalDistribution.cpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/src/ExportFeq.cpp (100%) rename {Circall_v0.2.0 => Circall_v1.0.0}/src/TxIndexer.cpp (100%) diff --git a/Circall_v0.2.0/.DS_Store b/Circall_v1.0.0/.DS_Store similarity index 100% rename from Circall_v0.2.0/.DS_Store rename to Circall_v1.0.0/.DS_Store diff --git a/Circall_v0.2.0/Circall_source.sh b/Circall_v1.0.0/Circall_source.sh similarity index 100% rename from Circall_v0.2.0/Circall_source.sh rename to Circall_v1.0.0/Circall_source.sh diff --git a/Circall_v0.2.0/Data/Circall_depdata_human.RData b/Circall_v1.0.0/Data/Circall_depdata_human.RData similarity index 100% rename from Circall_v0.2.0/Data/Circall_depdata_human.RData rename to Circall_v1.0.0/Data/Circall_depdata_human.RData diff --git a/Circall_v0.2.0/Data/test_read1.fasta.gz b/Circall_v1.0.0/Data/test_read1.fasta.gz similarity index 100% rename from Circall_v0.2.0/Data/test_read1.fasta.gz rename to Circall_v1.0.0/Data/test_read1.fasta.gz diff --git a/Circall_v0.2.0/Data/test_read2.fasta.gz b/Circall_v1.0.0/Data/test_read2.fasta.gz similarity index 100% rename from Circall_v0.2.0/Data/test_read2.fasta.gz rename to Circall_v1.0.0/Data/test_read2.fasta.gz diff --git a/Circall_v0.2.0/R/Circall_functions.R b/Circall_v1.0.0/R/Circall_functions.R similarity index 100% rename from Circall_v0.2.0/R/Circall_functions.R rename to Circall_v1.0.0/R/Circall_functions.R diff --git a/Circall_v0.2.0/R/Circall_simulator.R b/Circall_v1.0.0/R/Circall_simulator.R similarity index 100% rename from Circall_v0.2.0/R/Circall_simulator.R rename to Circall_v1.0.0/R/Circall_simulator.R diff --git a/Circall_v0.2.0/R/buildBSJdb.R b/Circall_v1.0.0/R/buildBSJdb.R similarity index 100% rename from Circall_v0.2.0/R/buildBSJdb.R rename to Circall_v1.0.0/R/buildBSJdb.R diff --git a/Circall_v0.2.0/R/createSqlite.R b/Circall_v1.0.0/R/createSqlite.R similarity index 100% rename from Circall_v0.2.0/R/createSqlite.R rename to Circall_v1.0.0/R/createSqlite.R diff --git a/Circall_v0.2.0/R/doPairEndFiltering.R b/Circall_v1.0.0/R/doPairEndFiltering.R similarity index 100% rename from Circall_v0.2.0/R/doPairEndFiltering.R rename to Circall_v1.0.0/R/doPairEndFiltering.R diff --git a/Circall_v0.2.0/R/doSingleEndFiltering.R b/Circall_v1.0.0/R/doSingleEndFiltering.R similarity index 100% rename from Circall_v0.2.0/R/doSingleEndFiltering.R rename to Circall_v1.0.0/R/doSingleEndFiltering.R diff --git a/Circall_v0.2.0/R/export.R b/Circall_v1.0.0/R/export.R similarity index 100% rename from Circall_v0.2.0/R/export.R rename to Circall_v1.0.0/R/export.R diff --git a/Circall_v0.2.0/R/getFdr.R b/Circall_v1.0.0/R/getFdr.R similarity index 100% rename from Circall_v0.2.0/R/getFdr.R rename to Circall_v1.0.0/R/getFdr.R diff --git a/Circall_v0.2.0/R/getPseudoCircRNAsequence.R b/Circall_v1.0.0/R/getPseudoCircRNAsequence.R similarity index 100% rename from Circall_v0.2.0/R/getPseudoCircRNAsequence.R rename to Circall_v1.0.0/R/getPseudoCircRNAsequence.R diff --git a/Circall_v0.2.0/R/load_packages.R b/Circall_v1.0.0/R/load_packages.R similarity index 100% rename from Circall_v0.2.0/R/load_packages.R rename to Circall_v1.0.0/R/load_packages.R diff --git a/Circall_v0.2.0/config.sh b/Circall_v1.0.0/config.sh similarity index 100% rename from Circall_v0.2.0/config.sh rename to Circall_v1.0.0/config.sh diff --git a/Circall_v0.2.0/include/EmpiricalDistribution.hpp b/Circall_v1.0.0/include/EmpiricalDistribution.hpp similarity index 100% rename from Circall_v0.2.0/include/EmpiricalDistribution.hpp rename to Circall_v1.0.0/include/EmpiricalDistribution.hpp diff --git a/Circall_v0.2.0/include/EquivalenceClassBuilder.hpp b/Circall_v1.0.0/include/EquivalenceClassBuilder.hpp similarity index 100% rename from Circall_v0.2.0/include/EquivalenceClassBuilder.hpp rename to Circall_v1.0.0/include/EquivalenceClassBuilder.hpp diff --git a/Circall_v0.2.0/include/ExportFeq.hpp b/Circall_v1.0.0/include/ExportFeq.hpp similarity index 100% rename from Circall_v0.2.0/include/ExportFeq.hpp rename to Circall_v1.0.0/include/ExportFeq.hpp diff --git a/Circall_v0.2.0/include/ReadExperiment.hpp b/Circall_v1.0.0/include/ReadExperiment.hpp similarity index 100% rename from Circall_v0.2.0/include/ReadExperiment.hpp rename to Circall_v1.0.0/include/ReadExperiment.hpp diff --git a/Circall_v0.2.0/include/SACollectorCircall.hpp b/Circall_v1.0.0/include/SACollectorCircall.hpp similarity index 100% rename from Circall_v0.2.0/include/SACollectorCircall.hpp rename to Circall_v1.0.0/include/SACollectorCircall.hpp diff --git a/Circall_v0.2.0/include/spdlog/details/format.h b/Circall_v1.0.0/include/spdlog/details/format.h similarity index 100% rename from Circall_v0.2.0/include/spdlog/details/format.h rename to Circall_v1.0.0/include/spdlog/details/format.h diff --git a/Circall_v0.2.0/install.sh b/Circall_v1.0.0/install.sh similarity index 100% rename from Circall_v0.2.0/install.sh rename to Circall_v1.0.0/install.sh diff --git a/Circall_v0.2.0/linux/.DS_Store b/Circall_v1.0.0/linux/.DS_Store similarity index 100% rename from Circall_v0.2.0/linux/.DS_Store rename to Circall_v1.0.0/linux/.DS_Store diff --git a/Circall_v0.2.0/linux/bin/Circall_bsj b/Circall_v1.0.0/linux/bin/Circall_bsj similarity index 100% rename from Circall_v0.2.0/linux/bin/Circall_bsj rename to Circall_v1.0.0/linux/bin/Circall_bsj diff --git a/Circall_v0.2.0/linux/bin/Circall_pseudo b/Circall_v1.0.0/linux/bin/Circall_pseudo similarity index 100% rename from Circall_v0.2.0/linux/bin/Circall_pseudo rename to Circall_v1.0.0/linux/bin/Circall_pseudo diff --git a/Circall_v0.2.0/linux/bin/Circall_wt b/Circall_v1.0.0/linux/bin/Circall_wt similarity index 100% rename from Circall_v0.2.0/linux/bin/Circall_wt rename to Circall_v1.0.0/linux/bin/Circall_wt diff --git a/Circall_v0.2.0/linux/bin/TxIndexer b/Circall_v1.0.0/linux/bin/TxIndexer similarity index 100% rename from Circall_v0.2.0/linux/bin/TxIndexer rename to Circall_v1.0.0/linux/bin/TxIndexer diff --git a/Circall_v0.2.0/linux/bin/buildBSJdb.R b/Circall_v1.0.0/linux/bin/buildBSJdb.R similarity index 100% rename from Circall_v0.2.0/linux/bin/buildBSJdb.R rename to Circall_v1.0.0/linux/bin/buildBSJdb.R diff --git a/Circall_v0.2.0/linux/bin/createSqlite.R b/Circall_v1.0.0/linux/bin/createSqlite.R similarity index 100% rename from Circall_v0.2.0/linux/bin/createSqlite.R rename to Circall_v1.0.0/linux/bin/createSqlite.R diff --git a/Circall_v0.2.0/linux/lib/libgcc_s.so.1 b/Circall_v1.0.0/linux/lib/libgcc_s.so.1 similarity index 100% rename from Circall_v0.2.0/linux/lib/libgcc_s.so.1 rename to Circall_v1.0.0/linux/lib/libgcc_s.so.1 diff --git a/Circall_v0.2.0/linux/lib/libgomp.so.1 b/Circall_v1.0.0/linux/lib/libgomp.so.1 similarity index 100% rename from Circall_v0.2.0/linux/lib/libgomp.so.1 rename to Circall_v1.0.0/linux/lib/libgomp.so.1 diff --git a/Circall_v0.2.0/linux/lib/libm.so.6 b/Circall_v1.0.0/linux/lib/libm.so.6 similarity index 100% rename from Circall_v0.2.0/linux/lib/libm.so.6 rename to Circall_v1.0.0/linux/lib/libm.so.6 diff --git a/Circall_v0.2.0/linux/lib/libsailfish_core.a b/Circall_v1.0.0/linux/lib/libsailfish_core.a similarity index 100% rename from Circall_v0.2.0/linux/lib/libsailfish_core.a rename to Circall_v1.0.0/linux/lib/libsailfish_core.a diff --git a/Circall_v0.2.0/linux/lib/libtbb.so b/Circall_v1.0.0/linux/lib/libtbb.so similarity index 100% rename from Circall_v0.2.0/linux/lib/libtbb.so rename to Circall_v1.0.0/linux/lib/libtbb.so diff --git a/Circall_v0.2.0/linux/lib/libtbb.so.2 b/Circall_v1.0.0/linux/lib/libtbb.so.2 similarity index 100% rename from Circall_v0.2.0/linux/lib/libtbb.so.2 rename to Circall_v1.0.0/linux/lib/libtbb.so.2 diff --git a/Circall_v0.2.0/linux/lib/libtbbmalloc.so b/Circall_v1.0.0/linux/lib/libtbbmalloc.so similarity index 100% rename from Circall_v0.2.0/linux/lib/libtbbmalloc.so rename to Circall_v1.0.0/linux/lib/libtbbmalloc.so diff --git a/Circall_v0.2.0/linux/lib/libtbbmalloc.so.2 b/Circall_v1.0.0/linux/lib/libtbbmalloc.so.2 similarity index 100% rename from Circall_v0.2.0/linux/lib/libtbbmalloc.so.2 rename to Circall_v1.0.0/linux/lib/libtbbmalloc.so.2 diff --git a/Circall_v0.2.0/linux/lib/libtbbmalloc_proxy.so b/Circall_v1.0.0/linux/lib/libtbbmalloc_proxy.so similarity index 100% rename from Circall_v0.2.0/linux/lib/libtbbmalloc_proxy.so rename to Circall_v1.0.0/linux/lib/libtbbmalloc_proxy.so diff --git a/Circall_v0.2.0/linux/lib/libtbbmalloc_proxy.so.2 b/Circall_v1.0.0/linux/lib/libtbbmalloc_proxy.so.2 similarity index 100% rename from Circall_v0.2.0/linux/lib/libtbbmalloc_proxy.so.2 rename to Circall_v1.0.0/linux/lib/libtbbmalloc_proxy.so.2 diff --git a/Circall_v0.2.0/src/CMakeLists.txt b/Circall_v1.0.0/src/CMakeLists.txt similarity index 100% rename from Circall_v0.2.0/src/CMakeLists.txt rename to Circall_v1.0.0/src/CMakeLists.txt diff --git a/Circall_v0.2.0/src/Circall_bsj.cpp b/Circall_v1.0.0/src/Circall_bsj.cpp similarity index 100% rename from Circall_v0.2.0/src/Circall_bsj.cpp rename to Circall_v1.0.0/src/Circall_bsj.cpp diff --git a/Circall_v0.2.0/src/Circall_pseudo.cpp b/Circall_v1.0.0/src/Circall_pseudo.cpp similarity index 100% rename from Circall_v0.2.0/src/Circall_pseudo.cpp rename to Circall_v1.0.0/src/Circall_pseudo.cpp diff --git a/Circall_v0.2.0/src/Circall_wt.cpp b/Circall_v1.0.0/src/Circall_wt.cpp similarity index 100% rename from Circall_v0.2.0/src/Circall_wt.cpp rename to Circall_v1.0.0/src/Circall_wt.cpp diff --git a/Circall_v0.2.0/src/EmpiricalDistribution.cpp b/Circall_v1.0.0/src/EmpiricalDistribution.cpp similarity index 100% rename from Circall_v0.2.0/src/EmpiricalDistribution.cpp rename to Circall_v1.0.0/src/EmpiricalDistribution.cpp diff --git a/Circall_v0.2.0/src/ExportFeq.cpp b/Circall_v1.0.0/src/ExportFeq.cpp similarity index 100% rename from Circall_v0.2.0/src/ExportFeq.cpp rename to Circall_v1.0.0/src/ExportFeq.cpp diff --git a/Circall_v0.2.0/src/TxIndexer.cpp b/Circall_v1.0.0/src/TxIndexer.cpp similarity index 100% rename from Circall_v0.2.0/src/TxIndexer.cpp rename to Circall_v1.0.0/src/TxIndexer.cpp diff --git a/Dockerfile b/Dockerfile index c1b8c17..006a6a8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,7 +6,7 @@ LABEL authors="Dat T Nguyen" \ ADD environment.yml / -ADD Circall_v0.2.0 /Circall +ADD Circall_v1.0.0 /Circall RUN conda install mamba -n base -c conda-forge -y