Could iCount xlsites support soft-clipping?

[TomSmithCGAT]

When using an aligner which is allowed to soft-clip the reads, this can error out with an index error at poss[idx] as len(read.query_length()) used to define idx will be greater than len(read.get_reference_positions(). Would it be possible for iCount to support use of aligners with soft-clipping?

iCount/iCount/mapping/xlsites.py

Lines 471 to 492 in 4260bae

	poss = read.get_reference_positions()
	if read.is_reverse:
	strand = '-'
	xlink_pos = poss[-1] + 1
	end_pos = poss[0]
	else:
	strand = '+'
	xlink_pos = poss[0] - 1
	xlink_pos = 1 if xlink_pos < 1 else xlink_pos # Case of neg. pos on circular MT
	end_pos = poss[-1]
	chrom = read.reference_name
	second_start, is_strange = _second_start(read, poss, strand, chrom, segmentation, gap_th)
	if is_strange:
	metrics.strange_recs += 1
	# Position of middle nucleotide. Because we can have spliced reads, middle position is
	# not necessarily the middle of region the read maps to. Take one nucleotide upstream
	# of center in case length is even, happens by default on + strand
	idx = read.query_length // 2 - 1 if (strand == '-' and read.query_length % 2 == 0) \
	else read.query_length // 2
	middle_pos = poss[idx]

As an example, BAM read:

NS500105:608:HHF3NBGXN:4:22601:5900:10521:N:0:GTCCGCrbc:TTAAGAC 147 chr1 189874 0 46S30M = 189693 -211 CACGACATCCTCCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGGGTGTGGGATGGTGGAGGGGTTTGAGA EEEAEA6EAAAAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE/EEEAEEAEEEEEEEEEAEEEEEEEEAAA/A AS:i:60 XS:i:98 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:96 YT:Z:CP NH:i:2

poss: [189873, 189874, 189875, 189876, 189877, 189878, 189879, 189880, 189881, 189882, 189883, 189884, 189885, 189886, 189887, 189888, 189889, 189890, 189891, 189892, 189893, 189894, 189895, 189896, 189897, 189898, 189899, 189900, 189901, 189902] (length=30)
idx:37