Mercurial > repos > iuc > medaka_variant
diff convert_VCF_info_fields.py @ 7:28c13c42de01 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
| author | iuc |
|---|---|
| date | Mon, 22 Feb 2021 19:59:00 +0000 |
| parents | aabb4e1c0b7b |
| children | edf6d4003fad |
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--- a/convert_VCF_info_fields.py Wed Feb 10 08:28:04 2021 +0000 +++ b/convert_VCF_info_fields.py Mon Feb 22 19:59:00 2021 +0000 @@ -15,7 +15,11 @@ def pval_to_phredqual(pval): - return round(-10 * log10(pval)) + try: + ret = round(-10 * log10(pval)) + except ValueError: + ret = 2147483647 # transform pval of 0.0 to max signed 32 bit int + return ret def parseInfoField(info): @@ -33,7 +37,7 @@ to_skip = set(['SC', 'SR']) for i, line in enumerate(in_vcf): if i == 1: - out_vcf.write("##convert_VCF_info_fields=0.1\n") + out_vcf.write("##convert_VCF_info_fields=0.2\n") if line[0:2] == "##": if line[0:11] == "##INFO=<ID=": id_ = line[11:].split(',')[0]