bam_to_bigwig.py BAM_FILE [BAM_FILE ...]
[-o, --bigwig_filename=<output file name>
 -t, --tempfile
 -k, --keep-tempfile
 -s, --ignore-secondary
 -q, --ignore-qc-fail
 -d, --ignore-optical-pcr-duplicate
 -u, --ignore-supplementary]

--bigwig_filename: if not given will save to <BAM file prefix>.bigwig.
--tempfile: If this is set, will use tempfile library to generate file names instead of using 
            <BAM file prefix>.wig and <BAM file prefix>.sizes.
--keep-tempfile: If this is set, will not delete the intermediate files <BAM file prefix>.wig 
                 and <BAM file prefix>.sizes.
--ignore-secondary: If this is set, rsem-bam2wig will ignore alignments with the 
                    "secondary alignment" flag bit 0x100 set.
--ignore-qc-fail: If this is set, rsem-bam2wig will ignore alignments with the 
                  "not passing quality controls" flag bit 0x200 set.
--ignore-optical-pcr-duplicate: If this is set, rsem-bam2wig will ignore alignments with the 
                                "PCR or optical duplicate" flag bit 0x400 set.
--ignore-supplementary: If this is set, rsem-bam2wig will ignore alignments with the 
                        "supplementary alignment" flag bit 0x800 set.

Han Lin, 2014.
Biomedical Electronics and Bioinformatics, National Taiwan University
National Agricultural Library, ARS, USDA