From edb9fd7a6734203070b623876e76ce4a0a164ed9 Mon Sep 17 00:00:00 2001 From: Saim Momin <64724322+SaimMomin12@users.noreply.github.com> Date: Tue, 16 Apr 2024 14:38:15 +0200 Subject: [PATCH] Fixed the unexpected behaviour due to `--assembly` parameter of `pairtools parse` (#5953) * Fixed Label Swapping issue * Debugging of --assembly name parameter * Eliminated conditional for assembly * Added a test for assembly name * Version bump for parse --- tools/pairtools/parse.xml | 18 +- ...output_parsed_pairs_sam_assemblyname.pairs | 600 ++++++++++++++++++ 2 files changed, 615 insertions(+), 3 deletions(-) create mode 100644 tools/pairtools/test-data/output_parsed_pairs_sam_assemblyname.pairs diff --git a/tools/pairtools/parse.xml b/tools/pairtools/parse.xml index 2a39a8198c2..9c78ac223b8 100644 --- a/tools/pairtools/parse.xml +++ b/tools/pairtools/parse.xml @@ -1,4 +1,4 @@ - + Find ligation pairs in alignments and create pairs. macros.xml @@ -8,7 +8,9 @@ pairtools parse '$sam_path' -c '$chroms_path' - $assembly + #if str($assembly_name).strip(): + --assembly '$assembly_name' + #end if -o '$output_parsed_pairs' --min-mapq '$min_mapq' --max-molecule-size '$max_molecule_size' @@ -27,7 +29,7 @@ - + @@ -112,6 +114,16 @@ + + + + + + + + + +