HISAT2 not reporting all splice sites?

[mattdoug]

I'm using HISAT2 (version 2.0.5) to try and find novel splice sites. Going through the SAM file it produces suggests that there are a number of alignments supporting the existence of splice junctions that are not being reported (i.e. the aren't in the file you get from using the "--novel-splicesite-outfile" option).

For example, the SAM record for one of the reads is:

SRR360120.14138165 83 V 12814114 60 9M1297N91M = 12813953 -261 ATCCCATGTCTTAATTAAACTTGTGGTAACTTTTAATGAATTAAACTTCTGATTTTGCCGATAAGCATATCATATGAAAAATACTAAAAATGTCGAAATGCC?CCCCDECEEEEC?D@FFDEECHHGEEGDEFHAGGIGJIIIHHGIJIGHCGDIJJGIIGHHCG@E?A9EAGIEGF@HHBFAJIGJHFF<FADBFF@@@ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:251 YT:Z:CP XS:A:- NH:i:1

The way it's split suggests that there is a splice junction at V:12814123-12815419, but there's no such entry in the file of reported splice sites.

For comparison, I ran TopHat (version 2.1.0) and it produced the same alignment for this read. The difference is that TopHat DOES report the expected splice junction at V:12,814,123-12,815,419.

So, is there some criteria I'm missing that causes HISAT2 to not report certain splice junctions, even if there are alignments supporting them?