diff --git a/libhts/__init__.py b/libhts/__init__.py index 9afa4cf56e017032f05517609eb3e0d2a8a16d2a..4f43948326f2bb70cdac29f4a30280255e871a8d 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 8a96ad515402ce002e03cbaf3bfe80e482b88532..45a339ce4af658ac1c4408a6ad9247337728906d 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