version 0.4.1

MikeAxtell · Mar 21, 2014 · ee75e2e · ee75e2e
1 parent 049c36b
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diff --git a/README b/README
@@ -1,7 +1,7 @@
 LICENSE
     ShortStack.pl
 
-    Copyright (C) 2012 Michael J. Axtell
+    Copyright (C) 2012-2013 Michael J. Axtell
 
     This program is free software: you can redistribute it and/or modify it
     under the terms of the GNU General Public License as published by the
@@ -23,15 +23,15 @@ SYNOPSIS
 CITATION
     If you use ShortStack in your work, please cite
 
-    Axtell MJ. (2012) ShortStack: Comprehensive annotation and
+    Axtell MJ. (2013) ShortStack: Comprehensive annotation and
     quantification of small RNA genes. In prep.
 
     As of this version release, a manuscript describing ShortStack is being
     revised. It might be published by the time you are reading this, so
     please check Pubmed before citing!
 
 VERSION
-    0.4.0 :: Released December 27, 2012
+    0.4.1 :: Released January 8, 2013
 
 AUTHOR
     Michael J. Axtell, Penn State University, mja18@psu.edu
@@ -236,7 +236,7 @@ OPTIONS
     for details. Default = 0.8. Allowed values between 0.5 and 1.
 
     --mindicerfrac [float] : Minimum fraction of mappings within Dicer size
-    range to annotate a locus as Dicer-derived. Default = 0.85. Allowed
+    range to annotate a locus as Dicer-derived. Default = 0.8. Allowed
     values between 0 and 1.
 
     --phasesize [integer] : Examine phasing only for clusters dominated by

diff --git a/README_Prep_bam b/README_Prep_bam
@@ -56,12 +56,14 @@ OPTIONS
 
 NOTES
   Input format and assumptions
+
     It is critical that the input sam, sam.gz, or bam file be sorted by read
     name. Additionally, it is assumed that read names are unique within the
     file. If either of these assumptions are not true, the results of this
     script are not reliable.
 
   Exisiting NH:i: tags
+
     If there are already NH:i: tags in the input data, they will be
     discarded and over-written by the script.
 

diff --git a/ShortStack.pl b/ShortStack.pl
@@ -6,8 +6,8 @@
 
 ###############MAIN PROGRAM BLOCK
 ##### VERSION
-my $version = "0.4.0";
-## December 27, 2012
+my $version = "0.4.1";
+## January 8, 2013
 ####
 
 ##### get options and validate them
@@ -3257,13 +3257,51 @@ sub get_star_coord {
 	@b_pos = sort {$b <=> $a} @b_pos;
     }
     my $c;
+
+    my $lkeymax;
+    my $lkeymin;
+    my $rkeymax;
+    my $rkeymin;
+
     foreach my $b (@b_pos) {
 	if($$brax_hash{$b} eq "\(") {
 	    push(@left,$b);
 	} elsif($$brax_hash{$b} eq "\)") {
 	    $c = pop @left;
 	    $leftpairs{$c} = $b;
+
+            if($lkeymax) {
+                if($c > $lkeymax) {
+                    $lkeymax = $c;
+                }
+            } else {
+                $lkeymax = $c;
+            }
+            if($lkeymin) {
+                if($c < $lkeymin) {
+                    $lkeymin = $c;
+                }
+            } else {
+                $lkeymin = $c;
+            }
+
 	    $rightpairs{$b} = $c;
+
+	    if($rkeymax) {
+                if($b > $rkeymax) {
+                    $rkeymax = $b;
+                }
+            } else {
+                $rkeymax = $b;
+            }
+            if($rkeymin) {
+                if($b < $rkeymin) {
+                    $rkeymin = $b;
+                }
+            } else {
+                $rkeymin = $b;
+            }
+
 	}
     }
 
@@ -3281,6 +3319,10 @@ sub get_star_coord {
 	    until(exists($leftpairs{$i})) {
 		--$i;
 		++$j;
+		if($i < ($lkeymin - 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_start = $leftpairs{$i} - $j;
 
@@ -3289,6 +3331,10 @@ sub get_star_coord {
 	    until(exists($leftpairs{$i})) {
 		++$i;
 		++$j;
+		if($i > ($lkeymax + 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_stop = $leftpairs{$i} + 2 + $j;
 
@@ -3298,6 +3344,10 @@ sub get_star_coord {
 	    until(exists($leftpairs{$i})) {
 		++$i;
 		++$j;
+		if($i > ($lkeymax + 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_start = $leftpairs{$i} + $j;
 
@@ -3306,6 +3356,10 @@ sub get_star_coord {
 	    until(exists($leftpairs{$i})) {
 		--$i;
 		++$j;
+		if($i < ($lkeymin - 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_stop = $leftpairs{$i} - 2 - $j;
 	}
@@ -3317,6 +3371,10 @@ sub get_star_coord {
 	    until(exists($rightpairs{$i})) {
 		--$i;
 		++$j;
+		if($i < ($rkeymin - 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_start = $rightpairs{$i} - $j;
 
@@ -3325,6 +3383,10 @@ sub get_star_coord {
 	    until(exists($rightpairs{$i})) {
 		++$i;
 		++$j;
+		if($i > ($rkeymax + 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_stop = $rightpairs{$i} + 2 + $j;
 	} elsif ($strand eq "-") {
@@ -3333,6 +3395,10 @@ sub get_star_coord {
 	    until(exists($rightpairs{$i})) {
 		++$i;
 		++$j;
+		if($i > ($rkeymax + 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_start = $rightpairs{$i} + $j;
 
@@ -3341,6 +3407,10 @@ sub get_star_coord {
 	    until(exists($rightpairs{$i})) {
 		--$i;
 		++$j;
+		if($i < ($rkeymin - 1)) {
+                    return "fail";
+                    last;
+                }
 	    }
 	    $star_stop = $rightpairs{$i} - 2 - $j;
 	}
@@ -6016,7 +6086,7 @@ =head1 LICENSE
 
 ShortStack.pl
 
-Copyright (C) 2012 Michael J. Axtell                                                             
+Copyright (C) 2012-2013 Michael J. Axtell                                                             
                                                                                                  
 This program is free software: you can redistribute it and/or modify                             
 it under the terms of the GNU General Public License as published by                             
@@ -6039,13 +6109,13 @@ =head1 CITATION
 
 If you use ShortStack in your work, please cite 
 
-Axtell MJ. (2012) ShortStack: Comprehensive annotation and quantification of small RNA genes.  In prep.
+Axtell MJ. (2013) ShortStack: Comprehensive annotation and quantification of small RNA genes.  In prep.
 
 As of this version release, a manuscript describing ShortStack is being revised.  It might be published by the time you are reading this, so please check Pubmed before  citing!
 
 =head1 VERSION
 
-0.4.0 :: Released December 27, 2012
+0.4.1 :: Released January 8, 2013
 
 =head1 AUTHOR
 
@@ -6154,7 +6224,7 @@ =head1 OPTIONS
 
 --minstrandfrac [float] : Minimum fraction of mappings to one or the other strand call a polarity for non-hairpin clusters.  Also the minimum fraction of "non-dyad" mappings to the sense strand within potential hairpins/miRNAs to keep the locus annotated as a hp or miRNA.  See below for details.  Default = 0.8.  Allowed values between 0.5 and 1.
 
---mindicerfrac [float] : Minimum fraction of mappings within Dicer size range to annotate a locus as Dicer-derived.  Default = 0.85.  Allowed values between 0 and 1.
+--mindicerfrac [float] : Minimum fraction of mappings within Dicer size range to annotate a locus as Dicer-derived.  Default = 0.8.  Allowed values between 0 and 1.
 
 --phasesize [integer] : Examine phasing only for clusters dominated by the indicated size range.  Size must be within the bounds described by --dicermin and --dicermax.  Set to 'all' to examine p-values of each locus within the Dicer range, in its dominant size.  Set to 'none' to suppress all phasing analysis.  Default = 21.  Allowed values between --dicermin and --dicermax.
 
@@ -6377,3 +6447,4 @@ =head2 Analysis of Phasing
 =cut
 
 
+