From bc6758c12c461c240b5d22ea1ff4798494681c65 Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Wed, 17 Jul 2019 10:53:34 +0200 Subject: [PATCH] More robust bam2bigwig.sh, increment version. --- libhts/__init__.py | 2 +- scripts/bam2bigwig.sh | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/libhts/__init__.py b/libhts/__init__.py index 9afa4cf..4f43948 100644 --- a/libhts/__init__.py +++ b/libhts/__init__.py @@ -1,4 +1,4 @@ -__version__ = 0.1 +__version__ = 0.2 from .libhts import ( aligner2min_mapq, gtf_2_genes_exon_lengths, diff --git a/scripts/bam2bigwig.sh b/scripts/bam2bigwig.sh index 8a96ad5..45a339c 100755 --- a/scripts/bam2bigwig.sh +++ b/scripts/bam2bigwig.sh @@ -50,6 +50,12 @@ bin_file=${2} # | sed 's/SN://g' | sed 's/LN://' \ # | bedops --chop 10 - \ # > Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/genome_binned_10.bed + +# Ensure we use a 3 columns minimal bed for bin_file: + +awk '{print $1"\t"$2"\t"$3}' ${bin_file} > "${workdir}/genome_binned.bed" +bin_file="${workdir}/genome_binned.bed" + lib_name=${3} orient=${4} # "F" is library type is normally stranded, "R" if it is reverse-stranded -- GitLab