Update README.md

Author: GregoryFaust

README.md

@@ -119,7 +119,7 @@ The **-M** flag is used for backward compatibility with older SAM/BAM files in w
 A **duplicate** read pair is defined as a pair that has the same *signature* for each mapped read as a previous read pair in the input SAM file.  The *signature* is comprised of the combination of the sequence name, strand, and the reference offset where the 5' end of the read would fall if the read were fully aligned (not clipped) at its 5' end.  The 5' aligned reference position is calculated using a combination of the POS field, the strand, and the CIGAR string.  This definition of *signature* matches that used by *Picard MarkDuplicates*.
 
 1. For pairs in which both reads are mapped, both signatures must match.
-2. For pairs in which only one side is mapped (an "orphan"), the signature of the mapped read must match a previously seen orphan. Starting with *samblaster* 0.1.25, the signatures of orphans ignore strand (all orphans are treated as if on forward strand). In an orphan pair, the unmapped read need not appear in the input file. In addition, mapped non-paired singleton (possible long) read alignments will be treated the same as an orphan pair with a missing unmapped read.
+2. For pairs in which only one side is mapped (an "orphan"), the signature of the mapped read must match a previously seen orphan. Starting with *samblaster* 0.1.25,  forward and reverse strand orphans/singletons are allowed to be duplicates of each other. In an orphan pair, the unmapped read need not appear in the input file. In addition, mapped non-paired singleton (possible long) read alignments will be treated the same as an orphan pair with a missing unmapped read.
 3. No doubly unmapped pair will be marked as a duplicate.
 4. Any *secondary* or *supplementary* alignment associated with a duplicate *primary* alignment will also be marked as a duplicate.