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Verified Commit a49b62ab authored by Mia Croiset's avatar Mia Croiset
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correct sort for build matrix test full

parent eb0ebae5
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......@@ -71,9 +71,6 @@ def pairs2matrix(
# tmp_dir=tmp_dir,
# )
cmd = 'grep -v ^# %s | sort -S 2G -k8,8n -k9,9n --parallel=1' % pairs_file
with open(pre_mat_file, "w") as fout:
fout.write(str(os.system(cmd)))
header_size = len(hio.get_pairs_header(pre_mat_file))
with open(pre_mat_file, "r") as pairs, open(mat_file, "w") as mat:
......
......@@ -17,7 +17,9 @@ process BUILD_MATRIX {
def args = task.ext.args ?: ''
"""
hicstuff_build_matrix.py -p ${idx_pairs} -f ${fragments_list} -t graal -o ${args}
grep -e ^# ${idx_pairs} > ${args}.pre.pairs
grep -v ^# ${idx_pairs} | sort -S 2G -k8,8n -k9,9n --parallel=1 >> ${args}.pre.pairs
hicstuff_build_matrix.py -p ${args}.pre.pairs -f ${fragments_list} -t graal -o ${args}
mv ${args} ${meta1.id}_${args}
"""
......
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