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Add option to save single mapped counts by side #248

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Add option to save single mapped counts by side #248

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33 changes: 28 additions & 5 deletions pairtools/cli/stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,11 @@
" all overlapping statistics. Non-overlapping statistics are appended to"
" the end of the file. Supported for tsv stats with single filter.",
)
@click.option(
"--single-mapped-by-side",
is_flag=True,
help="If specified, count single-mapped reads separately for read1 and read2.",
)
@click.option(
"--n-dist-bins-decade",
type=int,
Expand Down Expand Up @@ -115,7 +120,15 @@
)
@common_io_options
def stats(
input_path, output, merge, n_dist_bins_decade, bytile_dups, output_bytile_stats, filter, **kwargs
input_path,
output,
merge,
single_mapped_by_side,
n_dist_bins_decade,
bytile_dups,
output_bytile_stats,
filter,
**kwargs,
):
"""Calculate pairs statistics.

Expand All @@ -131,6 +144,7 @@ def stats(
input_path,
output,
merge,
single_mapped_by_side,
n_dist_bins_decade,
bytile_dups,
output_bytile_stats,
Expand All @@ -140,7 +154,15 @@ def stats(


def stats_py(
input_path, output, merge, n_dist_bins_decade, bytile_dups, output_bytile_stats, filter, **kwargs
input_path,
output,
merge,
single_mapped_by_side,
n_dist_bins_decade,
bytile_dups,
output_bytile_stats,
filter,
**kwargs,
):
if merge:
do_merge(output, input_path, n_dist_bins_decade=n_dist_bins_decade, **kwargs)
Expand Down Expand Up @@ -190,6 +212,7 @@ def stats_py(
filter = None

stats = PairCounter(
single_mapped_by_side=single_mapped_by_side,
n_dist_bins_decade=n_dist_bins_decade,
bytile_dups=bytile_dups,
filters=filter,
Expand All @@ -213,9 +236,9 @@ def stats_py(
stats.save(
outstream,
yaml=kwargs.get("yaml", False), # format as yaml
filter=first_filter_name
if not kwargs.get("yaml", False)
else None, # output only the first filter if non-YAML output
filter=(
first_filter_name if not kwargs.get("yaml", False) else None
), # output only the first filter if non-YAML output
)

if instream != sys.stdin:
Expand Down
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