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I am using FastaAlternateReferenceMaker and have a set of intervals ordered first by chromosome and then by their start positions. I have tried ordering chromosomes alphabetically(chr1, chr10, chr11,..) as well as numerically (chr1, chr2, chr3...) but the output fasta sequence returned is not in the same order as listed in interval file. I find that even the names target_1, target_2 etc are also not used as fasta headers in the output file. I am stuck with mapping the input intervals with the output fasta sequences.
Thanks in advance for all the help,