Master pub #542
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Master pub #542
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(cherry picked from commit 0b36db9)
When PS missing, the FORMAT and SAMPLE had different length now they are added with the default value "." When the --phase flag is present, the PS tag is added in FORMAT and the PS value is added to each sample, otherwise skipped When the --phase flag is present, the HP value is used to update the HET genotypes from "/" to "|" and order the genotype (i.e 0|1 or 1|0). Otherwise the default "/" is used Coverage bug: some cases we had None in the coverage list and it would cause an unhandled error, now we assess if there are 'None' values in the coverage before performing analysis
Possible edge case of a list [int,int,int,None], so far all seen cases have been either [int,int,int] or [None,None,None]
Fixing phasing + coverage bugs
default is the systems default (i.e linux = /tmp)
Temporary directory as argument
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Version 2.6.0