From 687c70df2e1dae90fc5260a7e3ef20998acae693 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicolai=20von=20K=C3=BCgelgen?= Date: Wed, 11 Oct 2023 14:01:21 +0200 Subject: [PATCH 1/2] Fix: #450 perform preprocessing on sorted vcf files --- .../wrappers/mehari/annotate_strucvars/wrapper.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py index 7b5f9386f..3d0bdd6ee 100644 --- a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py +++ b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py @@ -62,7 +62,7 @@ # Create auto-cleaned temporary directory export TMPDIR=$(mktemp -d) -trap "rm -rf $TMPDIR" EXIT +#trap "rm -rf $TMPDIR" EXIT # Run actual tools -------------------------------------------------------------------------------- @@ -81,9 +81,9 @@ bcftools sort -o $TMPDIR/fixed_bnd_to_inv.$num.vcf $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf # Fixup SVLEN=1 to SVLEN=. - sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf + sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv.$num.vcf # Fixup MELT header - sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf + sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv.$num.vcf # Add the missing "GT" tag echo '##FORMAT=' \ From 63dd518529475e17a353fda1617571233cddae22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicolai=20von=20K=C3=BCgelgen?= Date: Wed, 11 Oct 2023 14:10:44 +0200 Subject: [PATCH 2/2] uncommenting trap of TMPDIR --- snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py index 3d0bdd6ee..f2e9b415c 100644 --- a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py +++ b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py @@ -62,7 +62,7 @@ # Create auto-cleaned temporary directory export TMPDIR=$(mktemp -d) -#trap "rm -rf $TMPDIR" EXIT +trap "rm -rf $TMPDIR" EXIT # Run actual tools --------------------------------------------------------------------------------