Warnings about invalid chromosome intervals .

[Heather1999]

Thank you for developing this useful tool!
Hello,
I got warning requested interval outside of chromosome range:248387608-248388535 and the output was 0 KB.
I further samtools viewed the bam version of chr1:248387608-248388535 and got something like this:

LH00242:20:22F2FYLT3:2:1123:20593:12488 99 chr1 248388154 60 122M = 248388154 122 CACCATGCTGAGGCTGGCCTGTGGGGACAAAACCACCTATGAAACAGTGATGTATGTGTGCTGCGTTGCAATGCTGCTGATCCCCTTCTCGGTGGTGACTGCATCCTACACCAGGATTCTCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MC:Z:122M AS:i:117 XS:i:20 LO:Z:L_L RG:Z:AS_02N LH00242:20:22F2FYLT3:2:1123:20593:12488 147 chr1 248388154 60 122M = 248388154 -122 CACCATGCTGAGGCTGGCCTGTGGGGACAAAACCACCTATGAAACAGTGATGTATGTGTGCTGCGTTGCAATGCTGCTGATCCCCTTCTCGGTGGTGACTGCATCCTACACCAGGATTCTCA FFFFFFFFFFF5FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MC:Z:122M AS:i:117 XS:i:20 LO:Z:L_L RG:Z:AS_02N LH00242:20:22F2FYLT3:2:2259:39556:28654 83 chr1 248388155 60 151M = 248388088 -218 ACCATGCTGAGGCTGGCCTGTGGGGACAAAACCACCTATGAAACAGTGATGTATGTGTGCTGCGTTGCAATGCTGCTGATCCCCTTCTCGGTGGTGACTGCATCTTACACCAGGATTCTCATCACAGTGCATCAGATGACATCGGCTGAAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF5FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MC:Z:151M AS:i:151 XS:i:0 LO:Z:L_L RG:Z:AS_02N LH00242:20:22F2FYLT3:2:2157:18808:1417 81 chr1 248388156 60 151M = 248387995 -312 CCATGCTGAGGCTGGCCTGTGGGGACAAAACCACCTATGAAACAGTGATGTATGTGTGCTGCGTTGCAATGCTGCTGATCCCCTTCTCGGTGGTGACTGCATCCTACACCAGGATTCTCATCACAGTGCATCAGATGACATCGGCTGAAGG FFFFFFFFFFFFFFFFFFF

Is there anything wrong with my bam file?
Thank you!

[brentp]

Hi, sorry for the delay, if you're still having this problem, Can you show the header of the bam file, specifically the SN tag for chr1?
You could also show how you ran mosdepth