* switch the snp storage format again

diff --git a/genotypeizer b/genotypeizer
index 8c441cd7e41217d647b08df6cb1748e66e026ef8..06f6dd7921ab58254ee148ad3d7d879c6611f551 100755 (executable)
--- a/genotypeizer
+++ b/genotypeizer
@@ -174,36 +174,24 @@ while (($map_file,$ped_file) = splice @map_ped,0,2) {
                                         maternal_id   => $maternal_id,
                                         paternal_id   => $paternal_id,
                                        };
-         # do it this way to avoid eating memory
-         $samples{$individual_id} = \@snps;
-         if (@snps != 2*@map) {
-              die "The map file and the number of snps don't appear to match";
+         for my $snp_info (@map) {
+             $samples{$individual_id}{$snp_info->{rsid}} = [shift @snps, shift @snps];
+         }
+         if (@snps) {
+              die "The map file and the number of snps don't appear to match".join(' ',@snps)."were left over";
          }
      }
 }
 
 
 my %valid_snps;
+@valid_snps{map {s/^rs//; "rs$_";} @{$options{snps}}} = (1) x @{$options{snps}};
 
-if (defined $options{snps} and @{$options{snps}}) {
-    for my $snp_i (0..$#snp_order) {
-       for my $valid_snp (@{$options{snps}}) {
-           if ($snp_order[$snp_i]{rsid} =~ /(rs)?\Q$valid_snp\E/) {
-               $valid_snps{$snp_order[$snp_i]{rsid}} = $snp_i;
-               last;
-           }
-       }
-    }
-}
 
-my @snp_ordering;
+my @snp_ordering = map {$_->{rsid}} @snp_order;
+
 if (keys %valid_snps) {
-    @snp_ordering = sort {$valid_snps{$a} <=>
-                             $valid_snps{$b}
-                         } keys %valid_snps;
-}
-else {
-    @snp_ordering = map {$_->{rsid}} @snp_order;
+    @snp_ordering = grep {exists $valid_snps{$_}} @snp_ordering;
 }
 
 
@@ -223,7 +211,7 @@ if ($options{output_format} eq 'pedmap') {
            join("\t",
                 @{$extra_info{$individual_id}}{qw(family_id individual_id),
                                                    qw(paternal_id maternal_id sex phenotype)},
-                keys %valid_snps ? @{$samples{$individual_id}}[map {($_*2,$_*2+1)} @valid_snps{@snp_ordering}] : @{$samples{$individual_id}}
+                map {@{$_}} @{$samples{$individual_id}}{@snp_ordering}
                )."\n";
     }
 }