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Blaise LI
libhts
Commits
bc6758c1
Commit
bc6758c1
authored
Jul 17, 2019
by
Blaise Li
Browse files
More robust bam2bigwig.sh, increment version.
parent
1843ade5
Changes
2
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libhts/__init__.py
View file @
bc6758c1
__version__
=
0.
1
__version__
=
0.
2
from
.libhts
import
(
aligner2min_mapq
,
gtf_2_genes_exon_lengths
,
...
...
scripts/bam2bigwig.sh
View file @
bc6758c1
...
...
@@ -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
...
...
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