From 4d249f4c8eeb46785446b5d5d76fd081414921c6 Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Tue, 9 Apr 2024 10:06:59 +0200 Subject: [PATCH 1/5] Fixed Label Swapping issue --- tools/pairtools/parse.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/pairtools/parse.xml b/tools/pairtools/parse.xml index d87eb1e5273..2a39a8198c2 100644 --- a/tools/pairtools/parse.xml +++ b/tools/pairtools/parse.xml @@ -32,8 +32,8 @@ - - + + From 988391fb01f928ca513be661de5f9c1256bcb68c Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Tue, 16 Apr 2024 10:54:13 +0200 Subject: [PATCH 2/5] Debugging of --assembly name parameter --- tools/pairtools/parse.xml | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/tools/pairtools/parse.xml b/tools/pairtools/parse.xml index 2a39a8198c2..db7ade40fdb 100644 --- a/tools/pairtools/parse.xml +++ b/tools/pairtools/parse.xml @@ -8,7 +8,9 @@ pairtools parse '$sam_path' -c '$chroms_path' - $assembly + #if str( $assembly_selection.assembly_name_selector ) == "yes": + --assembly $assembly_name + #end if -o '$output_parsed_pairs' --min-mapq '$min_mapq' --max-molecule-size '$max_molecule_size' @@ -27,7 +29,16 @@ - + + + + + + + + + + From ef7ae57c4e7997420b936491b13f02aed2dacd71 Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Tue, 16 Apr 2024 11:32:30 +0200 Subject: [PATCH 3/5] Eliminated conditional for assembly --- tools/pairtools/parse.xml | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/tools/pairtools/parse.xml b/tools/pairtools/parse.xml index db7ade40fdb..1ed84c71d39 100644 --- a/tools/pairtools/parse.xml +++ b/tools/pairtools/parse.xml @@ -8,8 +8,8 @@ pairtools parse '$sam_path' -c '$chroms_path' - #if str( $assembly_selection.assembly_name_selector ) == "yes": - --assembly $assembly_name + #if $assembly_name: + --assembly '$assembly_name' #end if -o '$output_parsed_pairs' --min-mapq '$min_mapq' @@ -29,16 +29,7 @@ - - - - - - - - - - + From 8a37097f2f7d7b2096f1ddd47f99af722e63926b Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Tue, 16 Apr 2024 11:43:15 +0200 Subject: [PATCH 4/5] Added a test for assembly name --- tools/pairtools/parse.xml | 12 +- ...output_parsed_pairs_sam_assemblyname.pairs | 600 ++++++++++++++++++ 2 files changed, 611 insertions(+), 1 deletion(-) 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 1ed84c71d39..a1e97ca373a 100644 --- a/tools/pairtools/parse.xml +++ b/tools/pairtools/parse.xml @@ -8,7 +8,7 @@ pairtools parse '$sam_path' -c '$chroms_path' - #if $assembly_name: + #if str($assembly_name).strip(): --assembly '$assembly_name' #end if -o '$output_parsed_pairs' @@ -114,6 +114,16 @@ + + + + + + + + + + Date: Tue, 16 Apr 2024 12:13:41 +0200 Subject: [PATCH 5/5] Version bump for parse --- tools/pairtools/parse.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/pairtools/parse.xml b/tools/pairtools/parse.xml index a1e97ca373a..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