From c1e5aa73af5b004084e3cbf99f7af1c9b9e569cf Mon Sep 17 00:00:00 2001 From: Jin Yong Yoo Date: Fri, 21 Feb 2020 13:32:22 -0500 Subject: [PATCH 1/4] fixed bugs reported --- .gitignore | 2 ++ Changelog.md | 23 +++++++++++++++++++++++ bin/recognicer | 3 +++ bin/recognicer_df | 3 +++ bin/sicer | 3 +++ bin/sicer_df | 3 +++ sicer/src/find_islands_in_pr.py | 3 +++ 7 files changed, 40 insertions(+) create mode 100644 Changelog.md diff --git a/.gitignore b/.gitignore index d7fd078..6786e69 100644 --- a/.gitignore +++ b/.gitignore @@ -126,3 +126,5 @@ dmypy.json # End of https://www.gitignore.io/api/python #vscode .vscode + +.DS_Store \ No newline at end of file diff --git a/Changelog.md b/Changelog.md new file mode 100644 index 0000000..7474955 --- /dev/null +++ b/Changelog.md @@ -0,0 +1,23 @@ +# Changelog +All notable changes to this project will be documented in this file. + + +## [1.0.2] - 2020-02-21 +### Added +- Changelog file to keep track of changes to this project. + +### Fixed +- Fixed bug with outputting to an user-specified output directory. +- Fixed bug in `find_islands_in_pr` so that empty island lists do not trigger `IndexError`. + +## [1.0.1] - 2019-12-28 +### Fixed +- Fixed issue with calling BEDTools using `subprocess.call`. Instead, use `subprocess.Popen` to enable piping. +- Fixed method for getting CPU count + +## [1.0.0] - 2019-06-14 +### Added +- New version of SICER for improved user-friendliness and parallelization support +- Multiprocessing based on chromosomes +- RECOGNICER algorithm added +- Uses BEDTools to convert BAM file to BED automatically \ No newline at end of file diff --git a/bin/recognicer b/bin/recognicer index efe86ac..e3ef9ed 100644 --- a/bin/recognicer +++ b/bin/recognicer @@ -219,6 +219,9 @@ def main(): except: sys.exit("Output directory (%s) could not be created. Terminating program." % args.output_directory) + if not(os.path.isabs(args.output_directory)): + args.output_directory = os.path.join(curr_path, args.output_directory) + if args.cpu > cpu_available: args.cpu = cpu_available warnings.warn("The number of CPU cores entered is greater than the number of cores available for this process. Executing SICER with the maximum number of cores available.\n") diff --git a/bin/recognicer_df b/bin/recognicer_df index 85e27b2..94c1f52 100644 --- a/bin/recognicer_df +++ b/bin/recognicer_df @@ -210,6 +210,9 @@ def main(): except: sys.exit("Output directory (%s) could not be created. Terminating program.\n" % args.output_directory) + if not(os.path.isabs(args.output_directory)): + args.output_directory = os.path.join(curr_path, args.output_directory) + if (args.control_file is not None): if (len(args.control_file) > 2): sys.stderr.write("Error: Too many control file inputs. RECOGNICER accepts at max two files.\n") diff --git a/bin/sicer b/bin/sicer index 0f7620b..2a4d079 100755 --- a/bin/sicer +++ b/bin/sicer @@ -218,6 +218,9 @@ def main(): sys.stderr.write("Error: Gap size is not a multiple of window size.\n" % args.output_directory) sys.exit(1) + if not(os.path.isabs(args.output_directory)): + args.output_directory = os.path.join(curr_path, args.output_directory) + if args.cpu > cpu_available: args.cpu = cpu_available warnings.warn("The number of CPU cores entered is greater than the number of cores available for this process. Executing SICER with the maximum number of cores available.\n") diff --git a/bin/sicer_df b/bin/sicer_df index 0bef5e8..8f1c795 100755 --- a/bin/sicer_df +++ b/bin/sicer_df @@ -209,6 +209,9 @@ def main(): except: sys.exit("Output directory (%s) could not be created. Terminating program.\n" % args.output_directory) + if not(os.path.isabs(args.output_directory)): + args.output_directory = os.path.join(curr_path, args.output_directory) + if (args.control_file is not None): if (len(args.control_file) > 2): sys.stderr.write("Error: Too many control file inputs. SICER accepts at max two files.\n") diff --git a/sicer/src/find_islands_in_pr.py b/sicer/src/find_islands_in_pr.py index 3fffff1..baeb2d7 100644 --- a/sicer/src/find_islands_in_pr.py +++ b/sicer/src/find_islands_in_pr.py @@ -77,6 +77,9 @@ def combine_proximal_islands(islands, gap, window_size_buffer=3): """ proximal_island_dist = gap + window_size_buffer; + + if len(islands) == 0: + return [] final_islands = [] current_island = islands[0]; From ffa33f30d4240837c9c04cadf27cc518880d42f1 Mon Sep 17 00:00:00 2001 From: Jin Yong Yoo Date: Fri, 21 Feb 2020 13:54:49 -0500 Subject: [PATCH 2/4] deploy v1.0.2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 46a2b4c..84bea7c 100644 --- a/setup.py +++ b/setup.py @@ -14,7 +14,7 @@ setup( name='SICER2', - version='1.0.1', + version='1.0.2', description = 'SICER2, a redesigned and improved ChIP-seq broad peak calling tool', long_description='Redesigned and improved version of the original ChIP-seq broad peak calling tool SICER. Also contains Coarse-graining Approach for Identifying Broad Domains from ChIP-Enriched Regions (RECOGNICER)', url = 'http://zanglab.github.io/SICER2 ', From 7f7285f3dfb1af71d584dee85aeec4376cff91c8 Mon Sep 17 00:00:00 2001 From: Adetunji Date: Wed, 10 Jun 2020 09:49:48 -0500 Subject: [PATCH 3/4] . --- .gitignore | 0 .travis.yml | 0 LICENSE | 0 README.md | 0 bin/recognicer | 0 bin/recognicer_df | 0 docs/contact.md | 0 docs/img/sicer2_workflow.png | Bin docs/index.md | 0 docs/sicer2_output.md | 0 docs/workflow.md | 0 mkdocs.yml | 0 setup.py | 0 sicer/__init__.py | 0 sicer/lib/Background_island_probscore_statistics.py | 0 sicer/lib/GenomeData.py | 0 sicer/lib/Utility.py | 0 sicer/lib/__init__.py | 0 sicer/lib/associate_tags_with_regions.py | 0 sicer/main/run_RECOGNICER.py | 0 sicer/main/run_RECOGNICER_df.py | 0 sicer/main/run_SICER.py | 0 sicer/main/run_SICER_df.py | 0 sicer/src/__init__.py | 0 .../associate_tags_with_chip_and_control_w_fc_q.py | 0 sicer/src/coarsegraining.c | 0 sicer/src/coarsegraining.pyx | 0 sicer/src/compare_two_libraries_on_islands.py | 0 sicer/src/filter_islands_by_significance.py | 0 sicer/src/filter_raw_tags_by_islands.py | 0 sicer/src/find_islands_in_pr.py | 0 sicer/src/find_union_islands.py | 0 sicer/src/make_normalized_wig.py | 0 sicer/src/remove_redundant_reads.py | 0 sicer/src/run_make_graph_file_by_chrom.py | 0 sicer/utility/__init__.py | 0 .../calculate_cross_correlation_long_range.py | 0 sicer/utility/fragment-size-estimation.sh | 0 sicer/utility/make_graph_file.py | 0 test/control_1.bed | 0 test/control_2.bed | 0 test/test_scripts/__init__.py | 0 test/test_scripts/compare.py | 0 test/test_scripts/test.py | 0 test/travisCI/compare.py | 0 .../treatment_1-W200-FDR0.01-island.bed | 0 ...ent_1-W200-FDR0.01-islandfiltered-normalized.wig | 0 .../treatment_1-W200-FDR0.01-islandfiltered.bed | 0 .../treatment_1-W200-G600-FDR0.01-island.bed | 0 ...-W200-G600-FDR0.01-islandfiltered-normalized.wig | 0 ...treatment_1-W200-G600-FDR0.01-islandfiltered.bed | 0 ...nt_1-W200-G600-decreased-islands-summary-FDR0.01 | 0 ...nt_1-W200-G600-increased-islands-summary-FDR0.01 | 0 .../treatment_1-W200-G600-islands-summary | 0 .../treatment_1-W200-G600.scoreisland | 0 .../treatment_1-W200-cgnormalized.wig | 0 ...eatment_1-W200-decreased-islands-summary-FDR0.01 | 0 ...eatment_1-W200-increased-islands-summary-FDR0.01 | 0 .../treatment_1-W200-islands-summary | 0 .../expected_output/treatment_1-W200-normalized.wig | 0 .../expected_output/treatment_1-W200.cgisland | 0 .../treatment_1-and-treatment_2-W200-G600-summary | 0 .../treatment_1-and-treatment_2-W200-summary | 0 ...nt_1-vs-treatment_2-W200-G600-E1000-union.island | 0 .../treatment_1-vs-treatment_2-W200-union.island | 0 .../treatment_2-W200-FDR0.01-island.bed | 0 ...ent_2-W200-FDR0.01-islandfiltered-normalized.wig | 0 .../treatment_2-W200-FDR0.01-islandfiltered.bed | 0 .../treatment_2-W200-G600-FDR0.01-island.bed | 0 ...-W200-G600-FDR0.01-islandfiltered-normalized.wig | 0 ...treatment_2-W200-G600-FDR0.01-islandfiltered.bed | 0 .../treatment_2-W200-G600-islands-summary | 0 .../treatment_2-W200-G600.scoreisland | 0 .../treatment_2-W200-cgnormalized.wig | 0 .../treatment_2-W200-islands-summary | 0 .../expected_output/treatment_2-W200-normalized.wig | 0 .../expected_output/treatment_2-W200.cgisland | 0 test/treatment_1.bed | 0 test/treatment_2.bed | 0 79 files changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 .gitignore mode change 100644 => 100755 .travis.yml mode change 100644 => 100755 LICENSE mode change 100644 => 100755 README.md mode change 100644 => 100755 bin/recognicer mode change 100644 => 100755 bin/recognicer_df mode change 100644 => 100755 docs/contact.md mode change 100644 => 100755 docs/img/sicer2_workflow.png mode change 100644 => 100755 docs/index.md mode change 100644 => 100755 docs/sicer2_output.md mode change 100644 => 100755 docs/workflow.md mode change 100644 => 100755 mkdocs.yml mode change 100644 => 100755 setup.py mode change 100644 => 100755 sicer/__init__.py mode change 100644 => 100755 sicer/lib/Background_island_probscore_statistics.py mode change 100644 => 100755 sicer/lib/GenomeData.py mode change 100644 => 100755 sicer/lib/Utility.py mode change 100644 => 100755 sicer/lib/__init__.py mode change 100644 => 100755 sicer/lib/associate_tags_with_regions.py mode change 100644 => 100755 sicer/main/run_RECOGNICER.py mode change 100644 => 100755 sicer/main/run_RECOGNICER_df.py mode change 100644 => 100755 sicer/main/run_SICER.py mode change 100644 => 100755 sicer/main/run_SICER_df.py mode change 100644 => 100755 sicer/src/__init__.py mode change 100644 => 100755 sicer/src/associate_tags_with_chip_and_control_w_fc_q.py mode change 100644 => 100755 sicer/src/coarsegraining.c mode change 100644 => 100755 sicer/src/coarsegraining.pyx mode change 100644 => 100755 sicer/src/compare_two_libraries_on_islands.py mode change 100644 => 100755 sicer/src/filter_islands_by_significance.py mode change 100644 => 100755 sicer/src/filter_raw_tags_by_islands.py mode change 100644 => 100755 sicer/src/find_islands_in_pr.py mode change 100644 => 100755 sicer/src/find_union_islands.py mode change 100644 => 100755 sicer/src/make_normalized_wig.py mode change 100644 => 100755 sicer/src/remove_redundant_reads.py mode change 100644 => 100755 sicer/src/run_make_graph_file_by_chrom.py mode change 100644 => 100755 sicer/utility/__init__.py mode change 100644 => 100755 sicer/utility/calculate_cross_correlation_long_range.py mode change 100644 => 100755 sicer/utility/fragment-size-estimation.sh mode change 100644 => 100755 sicer/utility/make_graph_file.py mode change 100644 => 100755 test/control_1.bed mode change 100644 => 100755 test/control_2.bed mode change 100644 => 100755 test/test_scripts/__init__.py mode change 100644 => 100755 test/test_scripts/compare.py mode change 100644 => 100755 test/test_scripts/test.py mode change 100644 => 100755 test/travisCI/compare.py mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-FDR0.01-island.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered-normalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-island.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered-normalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-G600-decreased-islands-summary-FDR0.01 mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-G600-increased-islands-summary-FDR0.01 mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-G600-islands-summary mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-G600.scoreisland mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-cgnormalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-decreased-islands-summary-FDR0.01 mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-increased-islands-summary-FDR0.01 mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-islands-summary mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200-normalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-W200.cgisland mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-and-treatment_2-W200-G600-summary mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-and-treatment_2-W200-summary mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-G600-E1000-union.island mode change 100644 => 100755 test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-union.island mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-FDR0.01-island.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered-normalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-island.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered-normalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered.bed mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-G600-islands-summary mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-G600.scoreisland mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-cgnormalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-islands-summary mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200-normalized.wig mode change 100644 => 100755 test/travisCI/expected_output/treatment_2-W200.cgisland mode change 100644 => 100755 test/treatment_1.bed mode change 100644 => 100755 test/treatment_2.bed diff --git a/.gitignore b/.gitignore old mode 100644 new mode 100755 diff --git a/.travis.yml b/.travis.yml old mode 100644 new mode 100755 diff --git a/LICENSE b/LICENSE old mode 100644 new mode 100755 diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/bin/recognicer b/bin/recognicer old mode 100644 new mode 100755 diff --git a/bin/recognicer_df b/bin/recognicer_df old mode 100644 new mode 100755 diff --git a/docs/contact.md b/docs/contact.md old mode 100644 new mode 100755 diff --git a/docs/img/sicer2_workflow.png b/docs/img/sicer2_workflow.png old mode 100644 new mode 100755 diff --git a/docs/index.md b/docs/index.md old mode 100644 new mode 100755 diff --git a/docs/sicer2_output.md b/docs/sicer2_output.md old mode 100644 new mode 100755 diff --git a/docs/workflow.md b/docs/workflow.md old mode 100644 new mode 100755 diff --git a/mkdocs.yml b/mkdocs.yml old mode 100644 new mode 100755 diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 diff --git a/sicer/__init__.py b/sicer/__init__.py old mode 100644 new mode 100755 diff --git a/sicer/lib/Background_island_probscore_statistics.py b/sicer/lib/Background_island_probscore_statistics.py old mode 100644 new mode 100755 diff --git a/sicer/lib/GenomeData.py b/sicer/lib/GenomeData.py old mode 100644 new mode 100755 diff --git a/sicer/lib/Utility.py b/sicer/lib/Utility.py old mode 100644 new mode 100755 diff --git a/sicer/lib/__init__.py b/sicer/lib/__init__.py old mode 100644 new mode 100755 diff --git a/sicer/lib/associate_tags_with_regions.py b/sicer/lib/associate_tags_with_regions.py old mode 100644 new mode 100755 diff --git a/sicer/main/run_RECOGNICER.py b/sicer/main/run_RECOGNICER.py old mode 100644 new mode 100755 diff --git a/sicer/main/run_RECOGNICER_df.py b/sicer/main/run_RECOGNICER_df.py old mode 100644 new mode 100755 diff --git a/sicer/main/run_SICER.py b/sicer/main/run_SICER.py old mode 100644 new mode 100755 diff --git a/sicer/main/run_SICER_df.py b/sicer/main/run_SICER_df.py old mode 100644 new mode 100755 diff --git a/sicer/src/__init__.py b/sicer/src/__init__.py old mode 100644 new mode 100755 diff --git a/sicer/src/associate_tags_with_chip_and_control_w_fc_q.py b/sicer/src/associate_tags_with_chip_and_control_w_fc_q.py old mode 100644 new mode 100755 diff --git a/sicer/src/coarsegraining.c b/sicer/src/coarsegraining.c old mode 100644 new mode 100755 diff --git a/sicer/src/coarsegraining.pyx b/sicer/src/coarsegraining.pyx old mode 100644 new mode 100755 diff --git a/sicer/src/compare_two_libraries_on_islands.py b/sicer/src/compare_two_libraries_on_islands.py old mode 100644 new mode 100755 diff --git a/sicer/src/filter_islands_by_significance.py b/sicer/src/filter_islands_by_significance.py old mode 100644 new mode 100755 diff --git a/sicer/src/filter_raw_tags_by_islands.py b/sicer/src/filter_raw_tags_by_islands.py old mode 100644 new mode 100755 diff --git a/sicer/src/find_islands_in_pr.py b/sicer/src/find_islands_in_pr.py old mode 100644 new mode 100755 diff --git a/sicer/src/find_union_islands.py b/sicer/src/find_union_islands.py old mode 100644 new mode 100755 diff --git a/sicer/src/make_normalized_wig.py b/sicer/src/make_normalized_wig.py old mode 100644 new mode 100755 diff --git a/sicer/src/remove_redundant_reads.py b/sicer/src/remove_redundant_reads.py old mode 100644 new mode 100755 diff --git a/sicer/src/run_make_graph_file_by_chrom.py b/sicer/src/run_make_graph_file_by_chrom.py old mode 100644 new mode 100755 diff --git a/sicer/utility/__init__.py b/sicer/utility/__init__.py old mode 100644 new mode 100755 diff --git a/sicer/utility/calculate_cross_correlation_long_range.py b/sicer/utility/calculate_cross_correlation_long_range.py old mode 100644 new mode 100755 diff --git a/sicer/utility/fragment-size-estimation.sh b/sicer/utility/fragment-size-estimation.sh old mode 100644 new mode 100755 diff --git a/sicer/utility/make_graph_file.py b/sicer/utility/make_graph_file.py old mode 100644 new mode 100755 diff --git a/test/control_1.bed b/test/control_1.bed old mode 100644 new mode 100755 diff --git a/test/control_2.bed b/test/control_2.bed old mode 100644 new mode 100755 diff --git a/test/test_scripts/__init__.py b/test/test_scripts/__init__.py old mode 100644 new mode 100755 diff --git a/test/test_scripts/compare.py b/test/test_scripts/compare.py old mode 100644 new mode 100755 diff --git a/test/test_scripts/test.py b/test/test_scripts/test.py old mode 100644 new mode 100755 diff --git a/test/travisCI/compare.py b/test/travisCI/compare.py old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_1-W200-FDR0.01-island.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered-normalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-island.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered-normalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-decreased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-G600-decreased-islands-summary-FDR0.01 old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-increased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-G600-increased-islands-summary-FDR0.01 old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-islands-summary b/test/travisCI/expected_output/treatment_1-W200-G600-islands-summary old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-G600.scoreisland b/test/travisCI/expected_output/treatment_1-W200-G600.scoreisland old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-cgnormalized.wig b/test/travisCI/expected_output/treatment_1-W200-cgnormalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-decreased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-decreased-islands-summary-FDR0.01 old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-increased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-increased-islands-summary-FDR0.01 old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-islands-summary b/test/travisCI/expected_output/treatment_1-W200-islands-summary old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200-normalized.wig b/test/travisCI/expected_output/treatment_1-W200-normalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-W200.cgisland b/test/travisCI/expected_output/treatment_1-W200.cgisland old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-G600-summary b/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-G600-summary old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-summary b/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-summary old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-G600-E1000-union.island b/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-G600-E1000-union.island old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-union.island b/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-union.island old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_2-W200-FDR0.01-island.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered-normalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-island.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered-normalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered.bed old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-islands-summary b/test/travisCI/expected_output/treatment_2-W200-G600-islands-summary old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-G600.scoreisland b/test/travisCI/expected_output/treatment_2-W200-G600.scoreisland old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-cgnormalized.wig b/test/travisCI/expected_output/treatment_2-W200-cgnormalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-islands-summary b/test/travisCI/expected_output/treatment_2-W200-islands-summary old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200-normalized.wig b/test/travisCI/expected_output/treatment_2-W200-normalized.wig old mode 100644 new mode 100755 diff --git a/test/travisCI/expected_output/treatment_2-W200.cgisland b/test/travisCI/expected_output/treatment_2-W200.cgisland old mode 100644 new mode 100755 diff --git a/test/treatment_1.bed b/test/treatment_1.bed old mode 100644 new mode 100755 diff --git a/test/treatment_2.bed b/test/treatment_2.bed old mode 100644 new mode 100755 From 5b866f35f3f897832d58c588d76841671ad19312 Mon Sep 17 00:00:00 2001 From: Adetunji Date: Wed, 10 Jun 2020 09:51:02 -0500 Subject: [PATCH 4/4] update --- Changelog.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 Changelog.md diff --git a/Changelog.md b/Changelog.md old mode 100644 new mode 100755