Release/1.2.1 #61
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Release/1.2.1 #61
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Release/1.2.0
Merge pull request #44 from Illumina/release/1.2.0
Feature/change gq type
Addresses case where ALT allele(s) are one base, hence an indel and n…
…D/I]) but consistent genotypes (e.g 1 vs. 3)
…-for-indels Handles case where indels with opposite orientation (e.g. [I/D] vs. […
Bug/baf mnv handling
Uses GNU and OSX compatible mktemp
Applies change from BeadArrayFiles repository
Closed
CodeWithCare
reviewed
Apr 3, 2020
| @@ -55,6 +56,8 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): | |||
| sample_name (string): Name of sample | |||
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| Returns: | |||
| float: Minimum GenCall score (or None for empty arguments) | |||
| int: Minimum GenCall score, encoded as a phred quality (or None for empty arguments) | |||
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You will know better but isn't phred score a float?
| """ | ||
| return self._get_min_gencall_score(bpm_records) | ||
| min_gencall_score = self._get_min_gencall_score(bpm_records) | ||
| phred_quality_score = int(round(-10*log10(min(1.0, max(0.00001, 1 - min_gencall_score))))) |
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nvm I see the conversion here but not sure why an int conversion is required?
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you're right I don't think it needs it, will fix
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Nvm apparently it does. Prints one decimal place even though the type should be an int, not entirely sure without digging deeper but it passes the regression tests the way it is
| @@ -758,6 +758,8 @@ def __parse_file(self, manifest_file): | |||
| all_norm_ids = set() | |||
| for locus_idx in range(self.num_loci): | |||
| self.normalization_ids[locus_idx] += 100 * self.assay_types[locus_idx] | |||
| # To mimic the byte-wrapping behavior from GenomeStudio, AutoCall, IAAP take the mod of 256 | |||
| self.normalization_ids[locus_idx] %= 256 | |||
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