I find that querying a wig file using bigWigSummary requires the query start and end to use 0-based half open coordinates even though wig files are specified using 1-based close coordinates.
Is this as designed? Below is my evidence of the issue (if indeed it is an issue). Thanks Malcolm Cook # Given the following as the contents of my wigfile > cat t1.wig fixedStep chrom=chrA start=1 step=1 span=1 0.1 0.2 fixedStep chrom=chrA start=5 step=1 span=1 0.5 0.6 fixedStep chrom=chrA start=8 step=1 span=1 0.8 0.987654321 1 fixedStep chrom=chrA start=15 step=1 span=1 15 16 17 18 19 20 20 20 20 20 20 # and the following chromSize: > cat t1.chromsSizes.tab chrA 25 # I can produce a bigwig as > wigToBigWig t1.wig t1.chromsSizes.tab t1.bigWig # and can "roundtrip" it perfectly back to wig format, since there is no output from: bigWigToWig t1.bigWig stdout | diff t1.wig - So far so good. # But, when I try to extract the first 5 scores using 1-based indexing, the 1st value is returned incorrectly, viz: > bigWigSummary t1.bigWig chrA 0 5 5 0.2 0.2 n/a n/a 0.5 However, using 0 based indexing returns what I expect: > bigWigSummary t1.bigWig chrA 0 5 5 0.1 0.2 n/a n/a 0.5 Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
