Issue #10 - out by 1 error :-(

Author: tseemann

samclip

@@ -6,11 +6,21 @@ use Getopt::Long;
 use File::Basename;
 use Data::Dumper;
 
+#----------------------------------------------------------------------
+# the sitch
+#                      1     6     11    16    21    26  30
+# contig:              NNNNN NNNNN NNNNN NNNNN NNNNN NNNNN
+#
+# 11,20,+   10M                    xxxxx xxxxx
+# 11,20,+   6M4S                   xxxxx x----
+# 11,20,+   4S6M                   ----x xxxxx
+# 11,20,+   3S5M2S                 ---xx xxx--
+
 #----------------------------------------------------------------------
 # globals
 
 my $EXE = basename($0);
-my $VERSION = "0.2";
+my $VERSION = "0.3.0";
 my $AUTHOR = 'Torsten Seemann (@torstenseemann)';
 my $HOMEPAGE = "https://github.com/tseemann/samclip";
 
@@ -114,7 +124,7 @@ while (my $line = <ARGV>) {
     my $end = $start + length($sam[SAM_SEQ]) - 1;
     my $contiglen = $len->{$sam[SAM_RNAME]} or err("Reference", $sam[SAM_RNAME], "not in '$ref'");
     msg("CHROM=$sam[SAM_RNAME]:1-$contiglen POS=$start..$end CIGAR=$sam[SAM_CIGAR] HL=$HL SL=$SL SR=$SR HR=$HR max=$max)") if $debug;
-    unless ($start == 0 or $end >= $contiglen) {
+    unless ($start <= 1 or $end >= $contiglen) {
       if ($HL+$SL > $max or $HR+$SR > $max) {
         $removed++;
         next;