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Re^3: (OT) help reading a bgzip file

by Utilitarian (Vicar)
on May 03, 2011 at 14:50 UTC ( #902730=note: print w/ replies, xml ) Need Help??


in reply to Re^2: (OT) help reading a bgzip file
in thread (OT) help reading a bgzip file

Ah, OK, new one on me - anyway, what does the decompressed file that won't load into your editor say it is when you run file on it?

print "Good ",qw(night morning afternoon evening)[(localtime)[2]/6]," fellow monks."


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Re^4: (OT) help reading a bgzip file
by Anonymous Monk on May 03, 2011 at 16:04 UTC
    hi. it says what i put in the last post - that it is a gzip compressed data with extra field but when i read it with zless it is nonsense and contains mostly this string ^@ intermixed with ascii characters
      If file is really just a gzip file then try checking that it isn't corrupt
      gunzip -tv file.bgzip
      Looking at http://samtools.sourceforge.net/SAM1.pdf (which I think is the reference for the file format used by bgzip) it looks like the payload data (BAM) in the bgzip file is not ascii text - that would explain why you are seeing non-ascii text when you run it through zless.

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