Checking for truncated BAM files

[lamortenera]

Hello and thanks for the great tool.

This is more a feature request than an issue. We used bamtools 2.4 with a BAM file that happened to be truncated. We used both the GetNextAlignment function and the command-line:

bamtools convert -in truncated.bam -format sam

In both cases there is no warning or exception raised by bamtools. This could be dangerous in clinical application where data integrity is paramount.

I am not sure how this could be implemented, but when using samtools a warning is raised with truncated BAM files. Samtools checks that a certain sequence of bytes occurs at the end of a BAM file.