I'm reading in and splitting a tab-delimited .txt file:

while (<$IN>) {
    next if /^\s*@/;
    my @F = split("\t", $_);

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Whilst most of the content has a fixed column number, a number of fields are interchangeable - making it more difficult to process/handle them in the usual fashion ($F2 etc.).

What is the best way to now handle this? Luckily the field i'm interested in has a specific substring in it "MD:Z:". Could anybody provide some code or suggestions? I've thought about searching @F using grep for the MD:Z: pattern, although this seems like it may be slow and i'm not then sure how I would extract out the index of the match to use the information contained further - the plan being to split the pattern and interpret the information.

In reply to Handling variable column position by Anonymous Monk

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