X-Git-Url: https://git.donarmstrong.com/?p=bin.git;a=blobdiff_plain;f=genotypeizer;h=06f6dd7921ab58254ee148ad3d7d879c6611f551;hp=a4f2e4193079bb4a3ba40cea31a81c78899523db;hb=1886c7247cb16ed68a78cd5550b152689a465999;hpb=a000c62118b1e7e7f08957eb196651f8e5c08068

diff --git a/genotypeizer b/genotypeizer
index a4f2e41..06f6dd7 100755
--- 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{$individual_id}}[@valid_snps{@snp_ordering}] : @{$samples{$individual_id}}
+		 map {@{$_}} @{$samples{$individual_id}}{@snp_ordering}
 		)."\n";
     }
 }