change direct calls to samtools with Rsamtools

[asifzubair]

the system() calls to samtools might be unreliable and inefficient - use Rsamtools. While at it, change copy to file.copy also.

[asifzubair]

all system() calls have been removed, except for computing fraction of mtDNA reads in aligned reads. All copy/move commands are now executed by using file.copy or by appending the command to the calling script.

@ttriche , would it be possible to do the following using Rsamtools ?

command = paste("samtools view -F 4", bam.files, "| wc -l")
counts = mcmapply(system, command = command, intern = TRUE)
chrM_command = paste("samtools view -F 4", bam.files, "\"chrM\" | wc -l")
chrM_counts = mcmapply(system, command = chrM_command, intern = TRUE)
chrMvsOther = (strtoi(as.vector(chrM_counts))) / strtoi(as.vector(counts)) 

I wanted to eliminate these system calls which seem expensive.