updated example in docs - remove superfluous " "

epigen · Mar 30, 2023 · 68fa1b9 · 68fa1b9
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diff --git a/.gitignore b/.gitignore
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
diff --git a/CHANGES.txt b/CHANGES.txt
diff --git a/LICENSE b/LICENSE
diff --git a/README.rst b/README.rst
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
diff --git a/dockerfile b/dockerfile
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/img/LIQUORICE_new_workflow.png b/docs/img/LIQUORICE_new_workflow.png
diff --git a/docs/img/bias_correction_example.pdf b/docs/img/bias_correction_example.pdf
diff --git a/docs/img/bias_correction_example.png b/docs/img/bias_correction_example.png
diff --git a/docs/img/fitted_gaussians_example.pdf b/docs/img/fitted_gaussians_example.pdf
diff --git a/docs/img/fitted_gaussians_example.png b/docs/img/fitted_gaussians_example.png
diff --git a/docs/img/img/liquorice_logo.png b/docs/img/img/liquorice_logo.png
diff --git a/docs/img/img/liquorice_logo_fitted.png b/docs/img/img/liquorice_logo_fitted.png
diff --git a/docs/img/liquorice_logo.png b/docs/img/liquorice_logo.png
diff --git a/docs/img/liquorice_logo_fitted.png b/docs/img/liquorice_logo_fitted.png
diff --git a/docs/img/liquorice_logo_fitted_transparent.png b/docs/img/liquorice_logo_fitted_transparent.png
diff --git a/docs/img/liverDHS_selection_1.png b/docs/img/liverDHS_selection_1.png
diff --git a/docs/img/liverDHS_selection_2.png b/docs/img/liverDHS_selection_2.png
diff --git a/docs/img/liverDHS_selection_3.png b/docs/img/liverDHS_selection_3.png
diff --git a/docs/img/overlay_plot_example.pdf b/docs/img/overlay_plot_example.pdf
diff --git a/docs/img/overlay_plot_example.png b/docs/img/overlay_plot_example.png
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/source/conf.py b/docs/source/conf.py
diff --git a/docs/source/extra/google25ad18a36b820a71.html b/docs/source/extra/google25ad18a36b820a71.html
diff --git a/docs/source/index.rst b/docs/source/index.rst
diff --git a/docs/source/intro.rst b/docs/source/intro.rst
diff --git a/docs/source/liquorice.rst b/docs/source/liquorice.rst
diff --git a/docs/source/liquorice_commandline_tool.rst b/docs/source/liquorice_commandline_tool.rst
@@ -257,7 +257,7 @@ Example usage of LIQUORICE and the summary tool
     BEDS="./regionsets"
     HG38="./hg38"
 
-    for SAMPLE in "$SAMPLES"
+    for SAMPLE in $SAMPLES
     do
     LIQUORICE --bamfile "${BAMS}/${SAMPLE}.bam" --refgenome_fasta "${HG38}/hg38.fa" \
         --mappability_bigwig "${HG38}/hg38_mappability_75bp.bw" \

diff --git a/liquorice/LIQUORICE.py b/liquorice/LIQUORICE.py
diff --git a/liquorice/LIQUORICE_summary.py b/liquorice/LIQUORICE_summary.py
diff --git a/liquorice/__init__.py b/liquorice/__init__.py
diff --git a/liquorice/data/10000_random_training_regions_hg38.bed b/liquorice/data/10000_random_training_regions_hg38.bed
diff --git a/liquorice/data/Ctrl_17_testdata.bam b/liquorice/data/Ctrl_17_testdata.bam
diff --git a/liquorice/data/Ctrl_17_testdata.bam.bai b/liquorice/data/Ctrl_17_testdata.bam.bai
diff --git a/liquorice/data/hg38.blacklist.v2.0.bed b/liquorice/data/hg38.blacklist.v2.0.bed
diff --git a/liquorice/data/hg38.fa.mappability_100bp.subsetted_for_testdata.bw b/liquorice/data/hg38.fa.mappability_100bp.subsetted_for_testdata.bw
diff --git a/liquorice/data/hg38.p12.fa.fai b/liquorice/data/hg38.p12.fa.fai
diff --git a/liquorice/data/universal_DHSs.bed b/liquorice/data/universal_DHSs.bed
diff --git a/liquorice/tests/__init__.py b/liquorice/tests/__init__.py
diff --git a/liquorice/tests/test_LIQUORICE_commandline_tool_w_various_params.py b/liquorice/tests/test_LIQUORICE_commandline_tool_w_various_params.py
diff --git a/liquorice/tests/test_LIQUORICE_with_simple_testdata.sh b/liquorice/tests/test_LIQUORICE_with_simple_testdata.sh
diff --git a/liquorice/utils/AggregateAcrossRegions.py b/liquorice/utils/AggregateAcrossRegions.py
diff --git a/liquorice/utils/BiasFactorWeights.py b/liquorice/utils/BiasFactorWeights.py
diff --git a/liquorice/utils/BiasModel.py b/liquorice/utils/BiasModel.py
diff --git a/liquorice/utils/BinTableBiasFactors.py b/liquorice/utils/BinTableBiasFactors.py
diff --git a/liquorice/utils/CorrectForCNAs.py b/liquorice/utils/CorrectForCNAs.py
diff --git a/liquorice/utils/CoverageAndSequenceTablePreparation.py b/liquorice/utils/CoverageAndSequenceTablePreparation.py
diff --git a/liquorice/utils/FitGaussians.py b/liquorice/utils/FitGaussians.py
diff --git a/liquorice/utils/GlobalFragmentSize.py b/liquorice/utils/GlobalFragmentSize.py
diff --git a/liquorice/utils/MeanSequencingDepth.py b/liquorice/utils/MeanSequencingDepth.py
diff --git a/liquorice/utils/Plotting.py b/liquorice/utils/Plotting.py
diff --git a/liquorice/utils/RegionFilteringAndBinning.py b/liquorice/utils/RegionFilteringAndBinning.py
diff --git a/liquorice/utils/Workflows.py b/liquorice/utils/Workflows.py
diff --git a/liquorice/utils/__init__.py b/liquorice/utils/__init__.py
diff --git a/liquorice/utils/deeptoolsCountReadsPerBinDontCheckProperPairSAMflag.py b/liquorice/utils/deeptoolsCountReadsPerBinDontCheckProperPairSAMflag.py
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py