Read count in paired fastq bamhash computation

[stolpeo]

The read count of a bamhash computation of paired fastq files is not the same as the read count of a bamhash computation of the bam file the paired fastq files were converted from (as already mentioned in https://github.com/DecodeGenetics/BamHash/issues/4#issuecomment-157213763 ... actually it is half the amount of reads in the fastq bamhash computation):

$ bamhash_checksum_bam sample.bam
c0039f91693d4bfd	1749217454

$ bamhash_checksum_fastq sample_R1.fq sample_R2.fq
c0039f91693d4bfd	874608727

My expectation would be that the read count numbers are the same (I would expect the number from the bam bamhash computation). Is this behavior intentional? Otherwise it would be great if this could be fixed!

$ bamhash_checksum_fastq --version
bamhash_checksum_fastq version 1.1

Thanks, Oliver