How to use samtools idxstats <bamfile>

[serhatg]

Hi all,

I'd like to get the number of all reads in a bam file by using samtools idxstats <bamfile> in samtools library;however, the function only exists in bam_index.c, Is there any way of including a header file and calling this function to get the total reads number,

Thank you.

[JohnN]

Maybe "bamtools" could help (https://github.com/pezmaster31/bamtools)

e.g. $ bamtools stats -n YourFile.bam


**********************************************
Stats for BAM file(s):
**********************************************

Total reads: 412695
Mapped reads: 412695 (100%)
Forward strand: 204788 (49.6221%)
Reverse strand: 207907 (50.3779%)
Failed QC: 0 (0%)
Duplicates: 0 (0%)
Paired-end reads: 0 (0%)

[serhatg]

Thanks, I'll check it out;however, I would like call this function in my c++ application and get the number of total reads. You can use samtools in the same manner as: samtools idxstats <bamfile>, but I couldn't figure out a way of calling this function from my own app.

Cheers