Changes

Use <code>{{{param|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}

Use <code>{{{param|--in}}}</code> 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{{#if: {{{noStdin|}}} .|, unless your input file is stdin.}}

The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin|}}} |.|, unless your input file is stdin.}}

{{#if: {{{noStdin|}}}|This tool does not support input from stdin.|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}

{{#if: {{{noStdin|}}}|This tool does not support input from stdin.|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}