input File (
--in followed by your file name to specify the SAM/BAM input file.
The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
- is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
|SAM/BAM/Uncompressed BAM from file|
|SAM from stdin|
|BAM from stdin|
|Uncompressed BAM from stdin|
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the
samtools implementation so pipes between our tools and
samtools are supported.