From c22633037e5c6740098227df7a1b2ead1ef21ceb Mon Sep 17 00:00:00 2001 From: josephvalencia Date: Wed, 24 Apr 2019 12:00:08 -0500 Subject: [PATCH] seqLevel flag explanation --- README.md | 1 + src/test/TestTr.cpp | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c309482..424a461 100644 --- a/README.md +++ b/README.md @@ -124,6 +124,7 @@ Step 5: To run the visualization tool on chr1, pass LTR-RTs found in chr1 (.bed) | -plateauSeed | Minimum length of plateaus to be initially considered 'Keep' in merging step. | 10 | | -nThreads | Number of cores to be used. | 1 | | -gapTol | Number of base pairs that two plateaus can differ by in height/distance. Affects both plateau merging and pairing steps. | 200 | +|-seqLevel| Forces parallel execution on sequences within multi-FASTA file. Loads all sequences into memory|disabled| | -rawScores | prints the raw scores to a file called xxxxRawScores.txt under the output directory. | disabled | | -cleanedScores | prints the scores after merging to a file called xxxxCleanedScores.txt under the output directory. | disabled | | -nested | searches for nested elements. Results are stored in seperate files (marked as xxxxNestedDetector.bed) under the output directory | disabled | diff --git a/src/test/TestTr.cpp b/src/test/TestTr.cpp index 8f10b4d..6b1fdea 100644 --- a/src/test/TestTr.cpp +++ b/src/test/TestTr.cpp @@ -85,7 +85,7 @@ int main(int argc, char * argv[]) { "| -plateauSeed | Minimum length of plateaus to be initially considered 'Keep' in merging step. | 10 |\n" "| -nThreads | Number of cores to be used. | 1 |\n" "| -gapTol | Number of base pairs that two plateaus can differ by in height/distance. Affects both plateau merging and pairing steps. | 200 |\n" - "|-seqLevel| Forces parallel execution on equences within multi-FASTA file. Useful when entire geneome or multiple contigs all in one file.|disabled|\n" + "|-seqLevel| Forces parallel execution on sequences within multi-FASTA file. Loads all sequences into memory | disabled |\n" "| -rawScores | prints the raw scores to a file called xxxxRawScores.txt under the output directory. | disabled |\n" "| -cleanedScores | prints the scores after merging to a file called xxxxCleanedScores.txt under the output directory. | disabled |\n" "| -nested | searches for nested elements. Results are stored in seperate files (marked as xxxxNestedDetector.bed) under the output directory | disabled |\n"