Updating documentation for uniq to reflect changes to that command ahead of v1.2.5

Author: andrewdavidsmith

docs/content/uniq.md

@@ -18,18 +18,25 @@ have identical sequences and are mapped to the same genomic location
 chooses a random one to be the representative of the original DNA
 sequence.
 
+*Note* As of dnmtools v1.2.5, the option to use the sequence of reads
+when deciding if two reads are duplicates has been removed. In the
+context of analyzing bisulfite sequencing reads, this has the danger
+of introducing bias in downstream analyses. Also, in the same version
+the test for sorted order of reads cannot be disabled. Empirical tests
+showed very little improvement to speed when disabling this test.
+
 The `uniq` command can take reads sorted by (chrom, start, end,
 strand). If the reads in the input file are not sorted, run the
 following sort command using [samtools](https://samtools.github.io):
 
 ```shell
-$ samtools sort -O sam -o input-sorted.sam input.sam
+$ samtools sort -o reads_sorted.bam reads.bam
 ```
 
 Next, execute the following command to remove duplicate reads:
 
 ```shell
-$ dnmtools uniq -S duplicate-removal-stats.txt input-sorted.sam out-sorted.sam
+$ dnmtools uniq -S duplicate-removal-stats.txt reads_sorted.bam reads_uniq.bam
 ```
 
 ## Options
@@ -47,30 +54,26 @@ Output a histogram of duplication frequencies into the specified file
 for library complexity analysis.
 
 ```txt
- -s, -seq
-```
-Use the sequences of the reads to distinguish duplicates. This is not
-often recommended.
-
-```txt
- -A, -all-cytosines
+ -B, -bam
 ```
-Use all cytosines when comparing reads based on sequence (default:
-only use CpG sites). Only applies if `-s` (above) is used.
+The output is in BAM format. This is an option to help prevent
+accidentally writing BAM format to the terminal or through a pipe that
+expects plain text, e.g., SAM.
 
 ```txt
- -D, -disable
+ -stdout
 ```
-Disable testing if the reads are sorted by chromosome and
-position. This can be faster and is fine if you know your reads are
-sorted.
+Write the output to standard out. This is not done by default even
+without an output file given, because of the danger of writing BAM to
+the terminal or through a pipe unexpectedly. It is possible to write
+BAM redirected or through a pipe, but the `-stdout` argument is
+required.
 
 ```txt
  -s, -seed
 ```
-Random number seed. Which read to keep, among duplicates, is chosen
-randomly (default: 408). This option is typically only used for
-testing.
+Random number seed. Affects which read is kept among duplicates. The
+default seed is 408. This option is typically only used for testing.
 
 ```txt
  -v, -verbose