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.