[BioC] missing reads in alignerBAM

[Daniel.Berner at unibas.ch]

hi list
When I align the N reads contained in my Illumina fastq using  
NovoAlign, convert the resulting SAM output to BAM using Samtools, and  
then upload the BAM file using readAligned (ShortRead), the resulting  
AlignedRead object contains fewer than N reads. Reconverting the BAM  
to SAM and counting the lines using wc -l, however, indicates there  
are still N reads in the BAM. Hence it appears that during upload into  
R, some reads are lost. The AlignedRead object, however, will contain  
exactly N reads when I perform the alignment using bowtie instead of  
NovoAlign.
Any idea/comment on why reads are missing?
Thanks, Daniel