Hello all,

I have a gzipped file that contains a string of two bit binary codes. I'm attempting to read this in to do some work on the contents. However, when I attempt to use IO::Uncompress::AnyUncompress, each of the reads ends before the file end. Using gunzip -c | works just fine though. I've included a file snippet below and code. Is this a bug with IO::Uncompress::AnyUncompress? Is this something wrong with my code that attempts to use IO::Uncompress::AnyUncompress?

Edit: The file snippet below is where the read ends on line 899924 in each of the three files I'm processing. I don't know if those codes together add up to some sort of stop code.
1       899682  <B6>^E
1       899740  <B5>^E
1       899766  <B6>^E
1       899767  <B6>^E
1       899816  <B5>^E<B8>^E<BD>^E
1       899915  <B5>^E<B6>^E<B8>^E<BD>^E
1       899924  <B5>^E<B6>^E<B8>^E<BD>^E
1       900121  <B5>^E
1       900159  <B6>^E
1       900373  <B5>^E<B6>^E<B8>^E<BD>^E
1       900686  <B5>^E<B6>^E<BD>^E
1       900791  <B6>^E
1       900902  <B5>^E<B6>^E<B8>^E<BD>^E
1       900903  <B5>^E<B6>^E<B8>^E<BD>^E
1       901004  <B8>^E
1       901005  <B8>^E
1       901020  <B5>^E<B6>^E<B8>^E<BD>^E
1       901092  <B5>^E<B8>^E<BD>^E
1       901129  <B5>^E<B6>^E<B8>^E<BD>^E
1       901188  <B5>^E
1       901369  <B6>^E<B8>^E<BD>^E
1       901423  <B5>^E<BD>^E

[download]

Working code below results in line count 5042137. 
my $lineCount = 0;
foreach my $file (@whiFiles) {
    print "reading $file\n";

    open IN, "gunzip -c $file |" or die "Can't open file $!";
    while (<IN>) {
        next if ($_ =~ /^#/);
        chomp;
        my ($chr, $pos, $codes) = split(/\t/, $_);
        $lineCount++;
    }
    close IN;
}
print "Line count is $lineCount\n";

[download]

Non-working code below results in line count 13263.
my $lineCount = 0;
foreach my $file (@whiFiles) {
    print "reading $file\n";
    my $HANDLE = new IO::Uncompress::AnyUncompress($file,Transparent =
+> 1,
                                      AutoClose=>1) or die;

    while (<$HANDLE>) {
        next if ($_ =~ /^#/);
        chomp;
        my ($chr, $pos, $codes) = split(/\t/, $_);
        $lineCount++;
    }
    close $HANDLE;
}
print "Line count is $lineCount\n";

[download]

In reply to File read stopping prematurely by Ineffectual

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