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Picard: MarkDuplicates: account for missing trailing 0 #2094

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merged 3 commits into from
Oct 3, 2023
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Picard: MarkDuplicates: account for missing trailing 0 #2094

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c080b18
Proper fix for https://github.com/ewels/MultiQC/issues/2063
vladsavelyev Oct 1, 2023
23f27f4
[automated] Update CHANGELOG.md
multiqc-bot Oct 1, 2023
88b1a0a
Fix
vladsavelyev Oct 2, 2023
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6 changes: 2 additions & 4 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -17,10 +17,8 @@

### Module updates

- **FastQC**:
- Add top overrepresented sequences table ([#2075](https://github.com/ewels/MultiQC/pull/2075))
- **Picard**:
- Fix parsing mixed strings/numbers, account for trailing tab ([#2083](https://github.com/ewels/MultiQC/pull/2083))
- **FastQC**: Add top overrepresented sequences table ([#2075](https://github.com/ewels/MultiQC/pull/2075))
- **Picard**: MarkDuplicates: Fix parsing mixed strings/numbers, account for missing trailing `0` ([#2083](https://github.com/ewels/MultiQC/pull/2083), [#2094](https://github.com/ewels/MultiQC/pull/2094))

## [MultiQC v1.16](https://github.com/ewels/MultiQC/releases/tag/v1.16) - 2023-09-22

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35 changes: 17 additions & 18 deletions multiqc/modules/picard/MarkDuplicates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import math
import os
import re
from collections import OrderedDict
from collections import OrderedDict, defaultdict

from multiqc import config
from multiqc.plots import bargraph
Expand Down Expand Up @@ -80,7 +80,7 @@ def save_table_results(s_name, base_s_name, keys, parsed_data, recompute_merged_
for f in self.find_log_files(log_key, filehandles=True):
s_name = f["s_name"]
base_s_name = f["s_name"]
parsed_data = {}
parsed_lists = defaultdict(list)
keys = None
in_stats_block = False
recompute_merged_metrics = False
Expand Down Expand Up @@ -112,13 +112,14 @@ def save_table_results(s_name, base_s_name, keys, parsed_data, recompute_merged_
# Split the values columns
vals = l.rstrip("\n").split("\t")

# End of the METRICS table, or multiple libraries and we're not merging them
if len(vals) < 6 or (not merge_multiple_libraries and len(parsed_data) > 0):
# End of the METRICS table, or multiple libraries, and we're not merging them
if len(vals) < 6 or (not merge_multiple_libraries and len(parsed_lists) > 0):
parsed_data = {k: parsed_list[0] for k, parsed_list in parsed_lists.items()}
if save_table_results(s_name, base_s_name, keys, parsed_data, recompute_merged_metrics):
# Reset for next file if returned True
s_name = f["s_name"]
base_s_name = f["s_name"]
parsed_data = {}
parsed_lists = defaultdict(list)
keys = None
in_stats_block = False
recompute_merged_metrics = False
Expand All @@ -129,26 +130,24 @@ def save_table_results(s_name, base_s_name, keys, parsed_data, recompute_merged_
if keys and vals and len(keys) == len(vals):
for i, k in enumerate(keys):
# More than one library present and merging stats
if k in parsed_data:
if k in parsed_lists:
recompute_merged_metrics = True

val = vals[i].strip()
try:
val_float = float(val)
except ValueError:
# Account for string values
if k not in parsed_data: # First library
parsed_data[k] = val
else:
parsed_data[k] += "/" + val
parsed_lists[k].append(val)
else:
# Numerical values we can just add up
if k not in parsed_data: # First library
parsed_data[k] = val_float
elif isinstance(parsed_data[k], float):
parsed_data[k] += val_float
else:
parsed_data[k] += "/" + val
parsed_lists[k].append(val_float)

parsed_data = {}
for k in parsed_lists:
# Sometimes a numerical column will an empty string, so converting "" to 0.0
if all(isinstance(x, float) or x == "" for x in parsed_lists[k]):
parsed_data[k] = sum(0.0 if x == "" else x for x in parsed_lists[k])
else:
parsed_data[k] = "/".join(str(x) for x in parsed_lists[k])

# Superfluous function call to confirm that it is used in this module
# Replace None with actual version if it is available
Expand Down