Aligning reads to transcripts

[Sagnik Banerjee]

Hello,

I have a set of reads sequenced on PacBio. I wish to align those to a transcriptomic reference that contains sequences highly similar to one another (some have only 3-6 nucleotides of difference). There is no genome so I cannot allow for a spliced alignment. I set the alignIntronMax and alignIntronMin to 0 but the final alignments still contain some splices. How do I turn it off entirely?
Also is there a way I can generate an expanded cigar with = and X?

Thanks.
Sagnik