From a875b4e223c792efb2d895001e280e3db3696a3c Mon Sep 17 00:00:00 2001 From: emmarousseau Date: Mon, 18 Mar 2024 14:02:03 +0100 Subject: [PATCH] Adjust comments --- src/gffread/test.sh | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/src/gffread/test.sh b/src/gffread/test.sh index 698a6d7f..dcbad6bc 100755 --- a/src/gffread/test.sh +++ b/src/gffread/test.sh @@ -17,7 +17,7 @@ mkdir -p "$test_output_dir" echo "> Test 1 - Read annotation file, output GFF" "$meta_executable" \ - -E \ + --expose_dups \ --input "$test_dir/annotation.gff" \ -o "$test_output_dir/ann_simple.gff" @@ -31,8 +31,8 @@ echo ">> Check if output is empty" echo ">> Compare output to expected output" -# Not comparing header lines, they are not in the same order and reference file -# was created with a different version of gffread. +# Not comparing header lines as they are not in the same order +# (reference file was created with gffred version 11.8 instead of 12.7). diff <(grep -v '^#' "$expected_output_dir/ann_simple.gff") \ <(grep -v '^#' "$test_output_dir/ann_simple.gff") || \ (echo "Output file ann_simple.gff does not match expected output" && exit 1) @@ -57,8 +57,8 @@ echo ">> Check if output is empty" echo ">> Compare output to expected output" -# remove trailing semicolons from the files -# Difference in trailing semicolon presence might be due to reference output +# removing trailing semicolons from the files +# Difference in trailing semicolon presence possibly due to reference output # being generated by gffred version 11.8 instead of 12.7. sed -i 's/;$/''/' "$expected_output_dir/annotation.gtf" sed -i 's/;$/''/' "$test_output_dir/annotation.gtf" @@ -109,8 +109,7 @@ echo ">> Compare output to expected output" diff "$expected_output_dir/annotation.tbl" "$test_output_dir/annotation.tbl" || \ (echo "Output file annotation.tbl does not match expected output" && exit 1) -# reference output annotation.tbl was created manually since it was not included -# in the original test data. +# reference output annotation.tbl was created manually with gffread 0.12.7 ################################################################################