Closed jpuritz closed 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.
Setting an integer value works, but even 0.1 and 0.25 fail. Perhaps this is an integer vs. float issue?
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.
This should only see 2 haplotypes, no?
Again I would only expect to see 2.