Updated code documentation for final publication.

gglusman · Oct 19, 2017 · bec2c6b · bec2c6b
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Showing 4 changed files with 28 additions and 13 deletions.
diff --git a/bin/compareDMFs.pl b/bin/compareDMFs.pl
@@ -1,10 +1,14 @@
 #!/bin/env perl
 use strict;
-my $version = '170630';
+my $version = '171019';
 ####
 #
 # This software compares two genome fingerprints.
-# The method is described in Glusman et al., https://doi.org/10.1101/130807
+# The method is described in:
+#    Glusman G, Mauldin DE, Hood LE, Robinson M. Ultrafast Comparison of Personal
+#    Genomes via Precomputed Genome Fingerprints. Front Genet. 2017 Sep 26;8:136. doi:
+#    10.3389/fgene.2017.00136. eCollection 2017. PubMed PMID: 29018478; PubMed Central
+#    PMCID: PMC5623000.
 # 
 # Copyright 2017 by Gustavo Glusman, Institute for Systems Biology, Seattle, WA, USA.
 # It is provided by the Institute for Systems Biology as open source software,
@@ -43,7 +47,6 @@
 	next unless defined $dmf1->{$vl};
 	next if %todo && !$todo{$vl};
 	push @h, "L=$vl";
-	#my $pearson = correlation($folded0->{$L}, $folded1->{$L});
 	my $spearman = correlation(ranks($folded0->{$vl}), ranks($folded1->{$vl}));
 	push @f, sprintf("%.4f", $spearman);
 }

diff --git a/bin/computeDMF.pl b/bin/computeDMF.pl
@@ -1,10 +1,14 @@
 #!/bin/env perl
 use strict;
-my $version = '170630';
+my $version = '171019';
 ####
 #
 # This software computes a genome fingerprint for a single personal genome.
-# The method is described in Glusman et al., https://doi.org/10.1101/130807
+# The method is described in:
+#    Glusman G, Mauldin DE, Hood LE, Robinson M. Ultrafast Comparison of Personal
+#    Genomes via Precomputed Genome Fingerprints. Front Genet. 2017 Sep 26;8:136. doi:
+#    10.3389/fgene.2017.00136. eCollection 2017. PubMed PMID: 29018478; PubMed Central
+#    PMCID: PMC5623000.
 # 
 # Copyright 2017 by Gustavo Glusman, Institute for Systems Biology, Seattle, WA, USA.
 # It is provided by the Institute for Systems Biology as open source software,

diff --git a/bin/searchDMFs.pl b/bin/searchDMFs.pl
@@ -1,11 +1,15 @@
 #!/bin/env perl
 use strict;
-my $version = '171013';
+my $version = '171019';
 use FindBin qw($Bin);
 ####
 #
 # This software compares two sets of genome fingerprints.
-# The method is described in Glusman et al., https://doi.org/10.1101/130807
+# The method is described in:
+#    Glusman G, Mauldin DE, Hood LE, Robinson M. Ultrafast Comparison of Personal
+#    Genomes via Precomputed Genome Fingerprints. Front Genet. 2017 Sep 26;8:136. doi:
+#    10.3389/fgene.2017.00136. eCollection 2017. PubMed PMID: 29018478; PubMed Central
+#    PMCID: PMC5623000.
 # 
 # Copyright 2017 by Gustavo Glusman, Institute for Systems Biology, Seattle, WA, USA.
 # It is provided by the Institute for Systems Biology as open source software,
@@ -15,7 +19,7 @@
 ####
 #
 # The first parameters is the query set. It can include one or more fingerprints in serialized format. If a non-serialized fingerprint is used as query, it is automatically serialized using the fingerprint size of the target set.
-# The second parameter is the target set: a serialized collection of fingerprints.
+# The second parameter is the target set: a serialized collection of fingerprints. If absent, all-against-all comparisons are performed in the query set.
 #
 ####
 #
@@ -29,9 +33,9 @@
 die "Cannot find fpc (the search engine)\n" unless -s $fpc;
 my($query, $target) = @ARGV;
 unless ($query) {
-	print "Usage: searchDMFs.pl query target\n";
-	print "       searchDMFs.pl fingerprints/genome1.outn.gz target.fp\n";
-	print "       searchDMFs.pl query  (will perform all comparisons within the query data set)\n";
+	print "Usage: searchDMFs.pl fingerprints/genome1.outn.gz target.fp\n";
+	print "       searchDMFs.pl query-set target-set\n";
+	print "       searchDMFs.pl query-set  (will perform all comparisons within the query data set)\n";
 	exit;
 }
 

diff --git a/bin/serializeDMFs.pl b/bin/serializeDMFs.pl
@@ -1,10 +1,14 @@
 #!/bin/env perl
 use strict;
-my $version = '170707';
+my $version = '170719';
 ####
 #
 # This software collects genome fingerprints into a database for efficient searching.
-# The method is described in Glusman et al., https://doi.org/10.1101/130807
+# The method is described in:
+#    Glusman G, Mauldin DE, Hood LE, Robinson M. Ultrafast Comparison of Personal
+#    Genomes via Precomputed Genome Fingerprints. Front Genet. 2017 Sep 26;8:136. doi:
+#    10.3389/fgene.2017.00136. eCollection 2017. PubMed PMID: 29018478; PubMed Central
+#    PMCID: PMC5623000.
 # 
 # Copyright 2017 by Gustavo Glusman, Institute for Systems Biology, Seattle, WA, USA.
 # It is provided by the Institute for Systems Biology as open source software,