Updated WHAT_IS_NEW for RSEM v1.2.18

WHAT_IS_NEW

@@ -1,3 +1,10 @@
+RSEM v1.2.18
+
+- Only generate warning message if two mates of a read pair have different names 
+- Only parse attributes of a GTF record if its feature is "exon" to avoid unnecessary warning messages
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.17
 
 - Added error detection for cases such as a read's two mates having different names or a read is both alignable and unalignable

rsem-calculate-expression

@@ -518,7 +518,7 @@ The RNA-Seq protocol used to generate the reads is strand specific, i.e., all (u
 
 =item B<--bowtie2>
 
-Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM does not handle indel, local and discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. In particular, we use options '--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1' by default. "-0.1", the last parameter of '--score-min' is the negative value of the maximum mismatch rate allowed. This rate can be set by option '--bowtie2-mismatch-rate'. If reads are paired-end, we additionally use options '--no-mixed' and '--no-discordant'. (Default: off)
+Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM does not handle indel, local and discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. In particular, we use options '--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1' by default. The last parameter of '--score-min', '-0.1', is the negative of maximum mismatch rate. This rate can be set by option '--bowtie2-mismatch-rate'. If reads are paired-end, we additionally use options '--no-mixed' and '--no-discordant'. (Default: off)
 
 =item B<--sam>