#!/bin/bash -Ceuo pipefail
samtools idxstats HCC1395_BL.recalibrated.bam > idxstats.txt
x_map=$(grep -E "^chrX\s|^X\s" idxstats.txt | cut -f 3)
x_len=$(grep -E "^chrX\s|^X\s" idxstats.txt | cut -f 2)
y_map=$(grep -E "^chrY\s|^Y\s" idxstats.txt | cut -f 3)
y_len=$(grep -E "^chrY\s|^Y\s" idxstats.txt | cut -f 2)
awk -v xm="$x_map" -v xl="$x_len" -v ym="$y_map" -v yl="$y_len" '
BEGIN {
if (ym == 0 || yl == 0) {
print "XX"
} else {
x_cov = xm / xl
y_cov = ym / yl
ratio = x_cov / y_cov
if (ratio > 50.0) print "XX"
else print "XY"
}
}' > HCC1395_BL.sex.txt