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melisanahtar / ea-utils

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Incorrect total reads when using FIFO #26

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1.mkfifo test1.fastq && mkfifo test2.fq
2.cat source1.fastq>test1.fastq &
3.cat source2.fastq>test2.fastq &
4.fastq-mcf -o source1_filtered.fastq -o source2_filtered.fastq -C 100000 -t 
0.01 -l 50 --qual-mean 25 --max-ns 10 -q 15 adapters.fa test1.fastq test2.fastq 
>filter.stats

What is the expected output? What do you see instead?
The "Total reads: xxxxxx" should match the number of reads in source1.fastq and 
source2.fastq.

However the total reads is 100000 less than the correct value, matching the 
value specified in "-C".

What version of the product are you using? On what operating system?
ea-utils.1.1.2-537.tar.gz, Ubuntu 12.04

Please provide any additional information below.

Original issue reported on code.google.com by allenyuc...@gmail.com on 18 Oct 2013 at 8:09

GoogleCodeExporter commented 8 years ago 
Saw the change log in r546, which has corrected a bug in handling FIFO.

The bug no longer appears in the latest SVN checkout r665.

Original comment by allenyuc...@gmail.com on 18 Oct 2013 at 8:16

GoogleCodeExporter commented 8 years ago

Original comment by earone...@gmail.com on 13 Nov 2013 at 10:12