Fix SplitVariants task in TasksGenotypeBatch.wdl to be compatible with downstream analysis #647
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| # array and increments the counter for that array | ||
| line = line.strip('\n').split('\t') | ||
| line[4], line[5] = line[5], line[4] | ||
| SVTYPE_FIELD = 5 |
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Instead of reassigning SVTYPE_FIELD here, you should either set SVTYPE_FIELD to 5 at the beginning or (my preference) move the code that swaps the fields to right before you append a new line to current_lines
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This was addressed and the value was set to 5.
| 'ins': {'condition': lambda line: bca and line[SVTYPE_FIELD] == 'INS'} | ||
| } | ||
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| current_lines = {prefix: [] for prefix in condition_prefixes.keys()} | ||
| current_counts = {prefix: 0 for prefix in condition_prefixes.keys()} | ||
| current_suffixes = {prefix: 'a' for prefix in condition_prefixes.keys()} | ||
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| # Open the bed file and process |
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Please keep the comments throughout the script to help document the code's functionality
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More comments were added.
| # Checks which condition and prefix the current line matches and appends it to the corresponding | ||
| # array and increments the counter for that array | ||
| line = line.strip('\n').split('\t') | ||
| line[4], line[5] = line[5], line[4] |
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This needs a comment explaining what it's doing
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The SplitVariants task used to have some lines to switch columns 5 and 6 of the bed file output, which is read in downstream tasks of TrainRDGenotyping.GenotypePESR. This causes the TrainRDGenotyping.GenotypePESR to error out reporting.
Error: WARNING: Incorrect CNV type specified
1: stop("WARNING: Incorrect CNV type specified")
The python script splitvariants.py was modified to switch the columns to the appropriate order to be compatible with downstream analysis requirements.