Is the command bamtools filter missing -length parameter?

[hunglin59638]

In the file BWT.py, there is a function extract_alignments_with_length that attempts to filter alignments based on length. The filename sorted_bam_sorted_file_length_100 suggests that it should filter alignments with a length longer than 100 base pairs. However, it seems that the bamtools filter command used in the function doesn't utilize the -length parameter for length filtering.

Is this behavior expected, or should the -length parameter be incorporated into the bamtools filter command?

Relevant code

    def extract_alignments_with_length(self, length=10, map_quality=2):
        """
        Get alignments from bam file using length as a filter (default length=10, map_quality=2)
        TODO:: add filters (mapped, length, coverage and map_quality)
        """
        cmd="bamtools filter -in {input_bam} -out {output_bam}".format(
            input_bam=self.output_bam_sorted_file,
            output_bam=self.sorted_bam_sorted_file_length_100,
            length=length,
            map_quality=map_quality
        )
        # logger.info(cmd)
        subprocess.run(["bamtools","filter","-in",self.output_bam_sorted_file,"-out",self.sorted_bam_sorted_file_length_100])

[raphenya]

@hunglin59638, the items in the TODO:: are not used currently with the filter. Cheers.