enhance error checking around sam-dump
check result of chdir() in _dump_bam_from_sra
remove file name decision from dump_aligned_bam()
Catch exceptions in SraToBam::execute()

Especially exceptions coming out of validation
I think this should have changed in an earlier commit
Handle case where there are no unalinged reads
Break long line into two
Extract dump_unaligned_fastq()
enhance error reporting in dump_unaligned_fastq()
Move bam size checking outside of dump_aligned_bam()
Extract do_shellcmd() and use it
rename do_shellcmd to do_shellcmd_with_stdout
create do_shellcmd() function
Extract convert_fastq_to_bam()
place unlink($unaligned_fastq) in a more appropriate scope
extract merge_bams() function
extract check_ncbi_config() function
only check $sra_has_primary_alignment_info once
extract check_sra_database() function
Extract add_unaligned_reads_to_bam() and merge_unaligned_fastq_into_bam() functions