Extension alignments longer than 2000 bp

[marcelm]

Sometimes ssw_align() is asked to compute an alignment for a reference sequence longer than 2000 bp here:

strobealign/src/aln.cpp

Lines 35 to 43 in 8d3ef7e

	if (ref.length() > 2000){
	// std::cerr << "ALIGNMENT TO REF LONGER THAN 2000bp - REPORT TO DEVELOPER. Happened for read: " << query << " ref len:" << ref.length() << std::endl;
	aln.global_ed = 100000;
	aln.ed = 100000;
	aln.ref_offset = 0;
	aln.cigar = "*";
	aln.sw_score = -1000000;
	return aln;
	}

This gets triggered in the Drosophila test dataset for read @SRR6055476.50009. The chunk needs to start a couple of reads earlier. Putting reads @SRR6055476.50004 to @SRR6055476.50009 (paired end) in paired-end FASTQ files reproduces it reliably.

As discussed in #168