Previously, mono-exons, not classified as FSM or ISM, and contained inside a transcript, were classified as NIC. Now, only those mono-exons spaning a whole intron of the transcript are considered NIC (by intron retention), otherwise, they are considered genic. On the other hand, mono-exons starting before the beginning or ending after the end of the reference transcript were classified as genic, even if they span a whole intron. Now, these transcripts that start/finish before/after the reference transcript and span a whole intron are classified as NIC.
While doing this I found a bug in the classification of ISM mono-exons (probably affecting a very limited number of transcripts). This has also been fixed.
Previously, mono-exons, not classified as FSM or ISM, and contained inside a transcript, were classified as NIC. Now, only those mono-exons spaning a whole intron of the transcript are considered NIC (by intron retention), otherwise, they are considered genic. On the other hand, mono-exons starting before the beginning or ending after the end of the reference transcript were classified as genic, even if they span a whole intron. Now, these transcripts that start/finish before/after the reference transcript and span a whole intron are classified as NIC.
While doing this I found a bug in the classification of ISM mono-exons (probably affecting a very limited number of transcripts). This has also been fixed.