bam2html.util package¶

Submodules¶

bam2html.util.logger module¶

Module contents¶

bam2html.util.add_highlight_class(seq, index, n, base_stat, is_ref)[source]¶

bam2html.util.check_bam_index(bam, samtools)[source]¶

bam2html.util.check_samtools(samtools)[source]¶

bam2html.util.get_relative_index(ref_span, position, first_position)[source]¶

bam2html.util.highlight_span(span, relative_index, n, base_stat, is_ref)[source]¶

bam2html.util.parse_html(html, pos_list, new_title, css=None)[source]¶

bam2html.util.parse_position(position, column)[source]¶

chrom:pos
chrom:start-end
chrom:pos1,pos2,pos3

bam2html.util.run_cmd(cmd)[source]¶

bam2html.util.safe_open(filename, mode='r')[source]¶

bam2html.util.samtools_tview(bam, chrom, pos, reference=None, samtools='samtools', column=None)[source]¶