rmToTrackHub.pl doesn't check exit status of bedToBigBig

[diekhans]

Describe the issue

rmToTrackHub.pl exits 0 (success) even if bedToBigBed. falis

After discovering a corrupt bigbed align file, went back to look in the logs and found this:

Unsigned integer may not begin with minus sign (-) in field 13 line 2578 of t2t_h9_v01_hap1.fa.align.tsv, got\
 -1                                                                                                           

It is clear in the code that the exit status is not checked. Once I am able isolate the case that causes the bad .align.tsv, that will be another ticket.

# Make align file bigBed                                                                                                        
if ( $alignFile ) {                                                                                                             
$cmd = "$BEDTOBIGBED_PRGM -tab -as=$FindBin::RealBin/bigRmskAlignBed.as -type=bed3+14 $alignTSVFile $csizes $hubname/$alignFile.bb";                                                                                                                           
system($cmd);                                                                                                                   
}