bug in alignmentSieve --ATACshift

[njwehi]

Hi,

I performed the alignmentSieve --ATACshift, before that the bam file was:

R1 1107 chr1 3050133 40 35M 3050133 -35
R2 1187 chr1 3050133 40 35M 3050133 35

after the alignmentSieve, output is

R1 1107 chr1 3050133 40 30M 3050137 -26
R2 1187 chr1 3050137 40 31M 3050133 26

It seems that the alignmentSieve failed to consider the situation that Read1 and Read2 are completely or virtually complementary, making the fragment size (26bp) shorter than the read lengths (30bp, 31bp).

Thanks