+ export TMPDIR=/var/tmp
+ TMPDIR=/var/tmp
+ read lib regions
++ grep -w NBL04 bam
+ bam=/projects/rcorbettAlignment/NBL04/HS1783/33_lanes.rmdup.bam
+ gzip
+ for i in '$regions'
+ samtools view /projects/rcorbettAlignment/NBL04/HS1783/33_lanes.rmdup.bam 1:4175500-9251000
+ sort
+ read lib regions
++ grep -w NBL06 bam
+ bam=/projects/rcorbettAlignment/NBL06/HS1794/30_lanes.rmdup.bam
+ for i in '$regions'
+ samtools view /projects/rcorbettAlignment/NBL06/HS1794/30_lanes.rmdup.bam 17:53962000-54860000
+ sort
+ for i in '$regions'
+ samtools view /projects/rcorbettAlignment/NBL06/HS1794/30_lanes.rmdup.bam 11:70860000-71815000
+ read lib regions
++ grep -w NBL07 bam
+ bam=/projects/rcorbettAlignment/NBL07/HS1796/30_lanes.rmdup.bam
+ sort
+ for i in '$regions'
+ samtools view /projects/rcorbettAlignment/NBL07/HS1796/30_lanes.rmdup.bam 3:116900000-137960000
+ gzip
+ read lib regions