I am having difficulties running the preparePairs function in diffHiC, for a bam file that I aligned using bwa mem. The bam file has been sorted by name. When I call the function

preparePairs("test1.bam", param=param, file="test1.h5", dedup=TRUE, minq=10)

I get the following message:

diagnostics=preparePairs("test_sort.bam", hs.param, file="test.h5", dedup=TRUE, minq=10)
Error in chromosomes[[chrs[x]]] : subscript out of bounds

I appreciate any suggestion.

Thank you

It seems like you're using one of the older versions of diffHic, as that particular error message should not appear in the latest version. Anyway, this is probably caused by the fact that your list of restriction fragments in hs.param contains more chromosomes than are in the BAM file. This triggers an error in the release version (even the latest one), though the devel version has been modified to be more relaxed. For the time being, you should update to the latest release and remove all restriction fragments that are not present in the BAM file:

keep <- seqnames(hs.param$fragments)) %in%
    names(scanBamHeader("test_sort.bam")[[1]]$targets)
new.fragments <- hs.param$fragments[keep,]
hs.param <- reform(hs.param, fragments=new.fragments)