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chollenbeck / rad_haplotyper

MIT License
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Issue with haplotype rescues #28

Closed jpuritz closed 6 years ago

jpuritz commented 6 years ago

It looks the the -z parameter is not functioning properly. Here's a read out of the .hap.log for a particular individual using a -z 0.05 It appears to be failing at both the initial and rescue portion.

dDocent_Contig_4163: Unique Observed Haps:
$VAR1 = [
          'CGATT',
          'CAATT',
          'CGACC'
        ];
dDocent_Contig_4163: Problem- trying to fix...
dDocent_Contig_4163: Corrected Unique Observed Haps:
$VAR1 = [
          'CGACC',
          'CGATT',
          'CAATT'
        ];
dDocent_Contig_4163: Unable to rescue
dDocent_Contig_4163
$VAR1 = {
          'CGACC' => 9,
          'CGATT' => 9,
          'CGATG' => 1,
          'CAATT' => 1
        };
Expected haplotypes: 2
Observed haplotypes: 3

This should only see 2 haplotypes, no?

Failed, trying to recover...
dDocent_Contig_4163: Observed Haps:
$VAR1 = [
          'CGATT',
          'CAATT',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGATC',
          'CGATT',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGATT',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGATT',
          'CGACC',
          'CGATT',
          'CGATT',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGGTT',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGATT',
          'CGATT',
          'CGATT',
          'CGATT',
          'CAATT',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGATT',
          'CGATT',
          'CGGTT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGACC',
          'CAATT',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATT',
          'CGGTT',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGATG',
          'CGACC',
          'CGACC',
          'CGACC',
          'CGACC'
        ];
dDocent_Contig_4163: Unique Observed Haps:
$VAR1 = [
          'CGATT',
          'CAATT',
          'CGACC',
          'CGATC',
          'CGGTT'
        ];
dDocent_Contig_4163: Problem- trying to fix...
dDocent_Contig_4163: Corrected Unique Observed Haps:
$VAR1 = [
          'CGATC',
          'CGACC',
          'CGGTT',
          'CGATT',
          'CAATT'
        ];
dDocent_Contig_4163: Unable to rescue
dDocent_Contig_4163
$VAR1 = {
          'CGATC' => 1,
          'CGACC' => 61,
          'CGGTT' => 3,
          'CGATT' => 30,
          'CGATG' => 1,
          'CAATT' => 3
        };
Expected haplotypes: 2
Observed haplotypes: 5
Failed again...

Again I would only expect to see 2.

jpuritz commented 6 years ago

Setting an integer value works, but even 0.1 and 0.25 fail. Perhaps this is an integer vs. float issue?