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SAM Cat
========
Concatenate and convert SAM/BAM files quickly.
(c) Copyright in 2015 by David Weese.
Usage
-----
This tool reads one or many SAM/BAM files and outputs their concatenation as a SAM/BAM file.
The headers of more than one input file will be merged.
All formats will be detected from file extensions or input streams.
```
samcat one.bam two.sam three.bam -o concat.bam
```
Input and output formats can be arbitrary, i.e. to convert a SAM into a BAM file use:
```
samcat input.sam -o output.bam
```
If the output file name is omitted the result is written to stdout in SAM format, use ```-b``` to select BAM.
If ```-``` is used as input file name, the input is read from stdin.
```
cat input.sam | samcat -b - > output.bam
```
Additional Information
----------------------
As the BAM format is more compact than SAM and faster to parse the best performance will be reached with BAM files.
Contact
-------
For questions or comments, contact David Weese <dave.weese@gmail.com>.
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