BED File Information

This section provides BED file information.

BED File Specification

For information on BED file specifications, see the Genome Browser FAQ about BED format.

BED File Parsing Rules

• Any line in a BED file beginning with UPPER("scaffold") or UPPER("chr") is a line containing a genomic position. The line is to be parsed as such: chromosome name in column 1, start position in column 2 and end position in column 3.

• If the prefix of column 1 is UPPER("chr"), use the entire string upto the first white space as the chromosomeNameFromBedFile. For example, if the value in column 1 = "chr5", chromosomeNameFromBedFile is "chr5".

• If the prefix is UPPER("scaffold"), use the entire value of column 1 as the chromosomeNameFromBedFile. For example, if the value in column 1 = "scaffold12345", then the chromosomeNameFromBedFile is "scaffold12345").

• Look up the chromosome ID as W_EHA_CHROM_MAPPING.CHROMOSOME_WID by looking for hits on UPPER(W_EHA_CHROM_MAPPING.ALIAS) = UPPER(chromosomeNameFromBedFile).

• Reject the record if the value in column 2 (start position) or the value in column 3 (end position) are not valid numbers.

• Reject the record if the start position is greater than the end position.