Intersectbed/Coveragebed -Split Purify Exon?

all.reads.bam file records mapped RNA-seq reads data, including:

1. exon:exon junction
2. exon body
3. intron body
4. exon:intron junction

Q1: When calculating RPKM for given RefSeq gene including all the position reads, will the following command just calculate exon:exon junction reads and at same time ignore all other reads?coverageBED -abam all.reads.bam -b refseq.genes.BED12.bed -s -split >coverage.bed I'm confused by the mannual (Page 62):

When dealing with RNA-seq reads, for example, one typically wants to only tabulate coverage for the portions of the reads that come from exons (and ignore the interstitial intron seqeunce), The -split command allows for such coverage to be performed.

If "-split" is set, the exon:exon read (for example, 30M3000N46M") exists in -abam bam file, and the 3000N will NOT be wrongly intersected when running intersectBED command. But what about coverageBED command? I do hope the 3000N will be not calculated which makes sense, and I also hope the intron body reads and other reads will be NOT ignored.Q2: If one just want to calculate exon's RPKM, does it mean one should prepare -b file to record all the exon information, and run like this:coverageBED -abam all.reads.bam -b ...