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, 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.}}

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).}}

{|border="1" cellspacing="0" cellpadding="2"

{|border="1" cellspacing="0" cellpadding="2"

| <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code>

| <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code>

|-

|-

|SAM from stdin

|{{#if: {{{noStdin|}}} | |SAM from stdin}}

| <code>{{#if: {{{noParam|}}} | |--in}} -</code>

| <code>{{#if: {{{noParam|}}} | |--in}} -</code>

|-

|-