#Interleave
Interleaves huge files together. Useful for combining mate-pair FASTQ files.
##Usage
interleave takes as input 2 or more text files, and outputs to a file specified with the -o option (or standard output).
interleave [args] <file1> <file2> ...
args:
-l [num] - Lines from each file to interleave (default: 4)
-o [file] - File to output
##Installation
./configure
make
make check
make install
##Examples
Interleave 2 FASTQ mate-pair files:
> cat FC42GXXXXXX_1.fastq
@ROVE_0001:7:1:6:1934#0/1
ATCGTCGATAGATCGGAAGAGCGGTTCAGCAGGAAT
+ROVE_0001:7:1:6:1934#0/1
gggfggggggggggggggggeggggggggcggchgg
@ROVE_0001:7:1:6:54#0/1
ATCGTCGATAGATCGGAAGAGCGGTTCAGCAGGAAT
+ROVE_0001:7:1:6:54#0/1
gggggggggggghggf`gggggggffgcfgggggge
> cat FC42GXXXXXX_2.fastq
@ROVE_0001:7:1:6:1934#0/2
ATCGACGATAGATCGGAAGAGCGTCGTGTANGGAAA
+ROVE_0001:7:1:6:1934#0/2
ggeegedggggggggfgeggfgfggdbdbdEdTdb`
@ROVE_0001:7:1:6:54#0/2
ATCGACGATAGATCGGAAGAGCGTCGTGTANGGAAA
+ROVE_0001:7:1:6:54#0/2
gggggggcgggggggggggggggggggggcEffee^
> ./interleave FC42GXXXXXX_1.fastq FC42GXXXXXX_2.fastq
@ROVE_0001:7:1:6:1934#0/1
ATCGTCGATAGATCGGAAGAGCGGTTCAGCAGGAAT
+ROVE_0001:7:1:6:1934#0/1
gggfggggggggggggggggeggggggggcggchgg
@ROVE_0001:7:1:6:1934#0/2
ATCGACGATAGATCGGAAGAGCGTCGTGTANGGAAA
+ROVE_0001:7:1:6:1934#0/2
ggeegedggggggggfgeggfgfggdbdbdEdTdb`
@ROVE_0001:7:1:6:54#0/1
ATCGTCGATAGATCGGAAGAGCGGTTCAGCAGGAAT
+ROVE_0001:7:1:6:54#0/1
gggggggggggghggf`gggggggffgcfgggggge
@ROVE_0001:7:1:6:54#0/2
ATCGACGATAGATCGGAAGAGCGTCGTGTANGGAAA
+ROVE_0001:7:1:6:54#0/2
gggggggcgggggggggggggggggggggcEffee^
Interleave 2 text files, taking one line from each at a time.
> cat left-file.txt
A
B
> cat right-file.txt
X
Y
> ./interleave -l 1 -o merged.txt left-file.txt right-file.txt
> cat merged.txt
A
X
B
Y
Copyright (c) 2012-2013 Shiran Pasternak <shiranpasternak at gmail.com>
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