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update usage junctions extract test

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yang-yangfeng committed Jan 5, 2018
1 parent 812d3f1 commit 569030418b188ecdb48388074782521d245f6200
Showing with 8 additions and 5 deletions.
  1. +8 −5 tests/lib/junctions/test_junctions_extractor.cc
@@ -55,15 +55,18 @@ TEST_F(JunctionsExtractTest, ParseIncorrectOption) {
TEST_F(JunctionsExtractTest, Usage) {
ostringstream out, out2;
out << "Usage:\t\t" << "regtools junctions extract [options] indexed_alignments.bam" << endl;
out << "Usage:"
<< "\t\t" << "regtools junctions extract [options] indexed_alignments.bam" << endl;
out << "Options:" << endl;
out << "\t" << "-a INT\tMinimum anchor length. Junctions which satisfy a minimum "
"anchor length on both sides are reported. [8]" << endl;
out << "\t\t" << "-a INT\tMinimum anchor length. Junctions which satisfy a minimum \n"
<< "\t\t\t " << "anchor length on both sides are reported. [8]" << endl;
out << "\t\t" << "-i INT\tMinimum intron length. [70]" << endl;
out << "\t\t" << "-I INT\tMaximum intron length. [500000]" << endl;
out << "\t\t" << "-o FILE\tThe file to write output to. [STDOUT]" << endl;
out << "\t\t" << "-r STR\tThe region to identify junctions "
"in \"chr:start-end\" format. Entire BAM by default." << endl;
out << "\t\t" << "-r STR\tThe region to identify junctions \n"
<< "\t\t\t " << "in \"chr:start-end\" format. Entire BAM by default." << endl;
out << "\t\t" << "-s INT\tStrand specificity of RNA library preparation \n"
<< "\t\t\t " << "(0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR). [1]" << endl;
out << endl;
jc1.usage(out2);
ASSERT_EQ(out.str(), out2.str()) << "Error parsing as expected";

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