gmap-2020-09-12/util/fa_coords.pl.in

301 			    printf STDOUT ("%s:%d..",$chr_newname{$chr},$chrpos{$chr});
303 			    printf STDOUT ("%s:%d..",$chr,$chrpos{$chr});
305 			printf STDOUT ("%d (length = %d nt)",$chrpos{$chr}+$seglength-1,$seglength);
307 			    printf STDOUT (" (revcomp => %s:%d..%d)",$chr,$chrpos{$chr}+$seglength-1,$chrpos{$chr});
309 			    printf STDOUT (" (revcomp => %s:%d..%d)",$chr,$chrpos{$chr}+$seglength-1,$chrpos{$chr});
330 			$string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr});
332 			$string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr});
334 			$string .= sprintf("%d..%d",$chrpos{$chr},$chrpos{$chr}+$seglength-1);
347 			$lowest{$chr} = $chrpos{$chr};
348 		    } elsif ($chrpos{$chr} < $lowest{$chr}) {
349 			$lowest{$chr} = $chrpos{$chr};
351 		    $chrpos{$chr} += $seglength; # Used only when a header doesn't have a chrpos for this chr
392 		    $chrpos{$chr} = $2;
406 		    $chrpos{$chr} = $2;
419 			$chrpos{$chr} = $1;
420 			$chrpos{$chr} += 1;	# Because Celera uses 0-based coordinates
430 		    $chrpos{$chr} = $2;
462 		if (!defined($chrpos{$chr})) {
463 		    $chrpos{$chr} = 1;	# Start this contig at beginning of chromosome
489 		    printf STDOUT ("%s:%d..",$chr_newname{$chr},$chrpos{$chr});
491 		    printf STDOUT ("%s:%d..",$chr,$chrpos{$chr});
493 		printf STDOUT ("%d (length = %d nt)",$chrpos{$chr}+$seglength-1,$seglength);
495 		    printf STDOUT (" (revcomp => %s:%d..%d)",$chr,$chrpos{$chr}+$seglength-1,$chrpos{$chr});
497 		    printf STDOUT (" (revcomp => %s:%d..%d)",$chr,$chrpos{$chr}+$seglength-1,$chrpos{$chr});
519 		$string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr});
521 		$string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr});
523 		$string .= sprintf("%d..%d",$chrpos{$chr},$chrpos{$chr}+$seglength-1);
535 		$lowest{$chr} = $chrpos{$chr};
536 	    } elsif ($chrpos{$chr} < $lowest{$chr}) {
537 		$lowest{$chr} = $chrpos{$chr};
582 		$lowest{$chr} = $chrpos{$chr} = 1;
604 			$string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr});
606 			$string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr});
608 			$string .= sprintf("%d..%d",$chrpos{$chr},$chrpos{$chr}+$seglength-1);