search

RahmanTeamDevelopment / CoverView

A coverage and base/mapping quality evaluation tool for panel and whole exome next-generation sequencing
MIT License
4 stars 0 forks source link

CoverView fails when directional coverage output is requested #12

Closed andyrimmer closed 7 years ago

andyrimmer commented 7 years ago

When the following config is used

{
    "outputs": {  "profiles": true },
    "duplicates": true,
    "direction": true
}

CoverView fails with the following output

2017-05-19 10:22:15,797 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 292 - CoverView v1.2.0 started running 2017-05-19 10:22:15,799 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 314 - Running CoverView v1.2.0 with options 2017-05-19 10:22:15,799 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 315 - Namespace(bedfile='/Users/munz/root/work/projects/CoverView/data/GIAB/TSCP_coverviewInput.bed', config='config_error2.json', input='/Users/munz/root/work/projects/CoverView/data/GIAB/15680_sorted_picard.bam', output='giab') 2017-05-19 10:22:15,799 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 316 - {'only_fail_profiles': False, 'low_bq': 10, 'direction': True, 'transcript_db': None, 'low_mq': 20, 'duplicates': True, 'outputs': {'regions': True, 'gui': False, 'profiles': True}, 'pass': None, 'transcript': {'regions': True, 'profiles': True}} 2017-05-19 10:22:15,819 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 342 - There are 1471 target regions 2017-05-19 10:22:15,840 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 146 - Coverage metrics will be generated in a single process 2017-05-19 10:22:15,840 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 121 - Writing output headers 2017-05-19 10:22:15,873 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 152 - Processing cluster of regions spanning 1:17345363-17380526 2017-05-19 10:22:15,877 - DEBUG - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 152 - Loading reads into in-memory array Traceback (most recent call last): File "/Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py", line 345, in coverage_calculator.calculate_coverage_summaries() File "/Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py", line 185, in calculate_coverage_summaries self.write_outputs_for_region(target) File "/Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py", line 140, in write_outputs_for_region self.per_base_output.write_output(region_coverage_data) File "coverview/output.pyx", line 115, in coverview.output.PerBaseCoverageOutput.write_output (coverview/output.c:3350) per_base_summary.print_to_file( File "coverview/calculators.pyx", line 663, in coverview.calculators.PerBaseCoverageSummary.print_to_file (coverview/calculators.c:11104) output_line = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t[}\t{}\t[]\t{}\t{}\n".format( ValueError: Single '}' encountered in format string