docs/content/format.md: adding a description of the argument for when input is strict SAM format

Author: andrewdavidsmith

docs/content/format.md

@@ -19,16 +19,20 @@ into a single entry.  SAM/BAM files generated by abismal, Bismark and
 BSMAP can be formatted using the `format` command.
 
 An example use of this command to format a mapped reads file is:
-```shell
-$ dnmtools format -f abismal input.bam output.sam
+
+```console
+dnmtools format -f abismal input.bam output.sam
 ```
+
 Above, the file `input.sam` would have been generated by `abismal`.
 The file `output.bam` is the output, and an output file is required
 here unless the `-stdout` argument is specified (see below). Another
 example:
-```shell
-$ dnmtools format -f abismal -t 8 -B input.bam output.bam
+
+```console
+dnmtools format -f abismal -t 8 -B input.bam output.bam
 ```
+
 This will use 8 threads because of the `-t 8` and will produce output
 in BAM format because of the `-B` flag (not the filename of the
 output).
@@ -94,6 +98,13 @@ unlimited). Normally this parameter is determined during read mapping,
 but `format` can also reject reads that are in opposing strands in the
 same chromosome but map more than this many bases apart.
 
+```txt
+-S, -sam
+```
+The input follows SAM standards for orientation, where reads that map to the
+reverse complement of the reference genome are stored as their reverse
+complement in the SAM/BAM file.
+
 ```txt
 -F, -force
 ```