Paired-end reads in BAM files

Hi,

I was trying to run flux-capacitor with a BAM file with paired-reads and I get an error saying that "Annotation mapping PAIRED requires a paired-end read descriptor!". Then I ran flux-capacitor again with the --read-descriptor=PAIRED option and I got an error saying that I cannot use the read-descriptor option with BAM files:
[ERROR] You cannot specify the read descriptor when using BAM input files.

Is this a bug or am I using flux-capacitor with the wrong options?

Thanks,

Nuno Fonseca

flux-capacitor --force --annotation tests/data/reference/homo_sapiens/chr19.gtf -i test4/tophat1/PE1.pe.hits.bam --annotation-mapping PAIRED --threads 1 -p test4/tophat1/PE1.pe.hits.bam.par -o test4/tophat1/flux_cap/PE1.flux_cap.trans.tsv.gtf
Flux-Capacitor v1.2.3-20121129021848 (Flux Library: 1.20-20121129021848)

[PRE-CHECK] I am checking availability of the required lpsolve JNI libs.
[PRE-CHECK] * successfully loaded lpsolve JNI (version 5.5,release 0,build 14)

[ERROR] Annotation mapping PAIRED requires a paired-end read descriptor!