verkkofillet.pp.find_reads_intra_telo

verkkofillet.pp.find_reads_intra_telo(tel, lineNum, scfmap='assembly.scfmap', layout='assembly.homopolymer-compressed.layout', gap_bed='stats/assembly.gaps.bed')

Find the reads support for the additional artifical sequences outside of the telomere.

Parameters:

• tel – The DataFrame containing the telomere information. This is the output of the find_intra_telo function.

• lineNum – The line number of the telomere. This is the index of the tel DataFrame.

• scfmap – The path to the scfmap file. Default is “assembly.scfmap”.

• layout – The path to the layout file. Default is “6-layoutContigs/unitig-popped.layout”.

Returns:

The DataFrame containing the readName, start_hpc, end_hpc, start, end, and type columns.