Contig

Creating SBP files ("SAM BreakPoint") from bwa-mem-aligned reads. These contain base-pair resolution information about breakpoints detected between chimeric segment.

1. SAMReader.py: takes SAM file, finds breakpoints for every line. (note, contigs span two lines). Writes pSBP file, which has the columns, ''' "query_name", "ref_name", "bp_pos", "end_pos", "ref_pos", "is_reverse", "is_left"''' (ref_pos is refrerence position of nearest mapped position to breakpoint)
2. BreakPointParser.R: Creates SBP file by merging a pair of pSBP lines based on query_name to create the SBP. Segments Sa and Sb correspond to left and right end of chimeric segment, resp. Multiple breakpoints per contig result in multiple (N-1) lines in BreakpointParser
3. SBPprocessor.R: creates simple BPC (aka rSBP = reduced SBP) file with chromA/chromB breakpoint positions (1-index format). A qSBP file is optionally generated which gives information about paired breakpoints (more than one breakpoint per contig)

Tigra-sv sometimes creates pathologically long contig names which makes samtools (and pysam) choke. qname_convert.py shortens QNAMEs in all SAM files to a hex string using an MD5 hash.