Updating documentation for changes introduced in v1.4.0

Author: andrewdavidsmith

docs/content/bsrate.md

@@ -171,7 +171,12 @@ This option will generate a histogram of conversion rate per read,
 printed to the terminal. This option is correct as of v1.4.0.
 
 ```txt
- -p, -per-read
+ -b, -bins
 ```
 Assming the `-p` option is used, this option determines the number of
 bins in the histogram. This option is correct as of v1.4.0.
+
+```txt
+ -S, -summary
+```
+Write a summary of information gathered during the run to this file.

docs/content/cleanhp.md

@@ -16,7 +16,7 @@ output filename prefix [required]
 ```txt
  -s, -stat
 ```
- stats output filename [required]
+stats output filename [required]
 ```txt
  -h, -hairpin
 ```
@@ -28,17 +28,20 @@ check for hairpin contamination
 ```txt
  -n, -nreads
 ```
- number of reads in initial check
+number of reads in initial check
 ```txt
  -c, -cutoff
 ```
- cutoff for calling an inverse duplication(default: 0.95)
+cutoff for calling an inverse duplication(default: 0.95)
 ```txt
  -i, -ignore
 ```
 length of read name suffix to ignore when matching
 ```txt
  -v, -verbose
 ```
-print more run info to STDERR while the program is running
-
+print more run info to the terminal while the program is running
+```txt
+ -h, -hist
+```
+write a histogram of hairpin matches to this file

docs/content/counts.md

@@ -171,3 +171,8 @@ merge data as symmetric CpGs.
 -v, -verbose
 ```
 Report more information while the program is running.
+
+```txt
+-progress
+```
+Show progress while the program is running.

docs/content/hmr.md

@@ -174,5 +174,5 @@ testing (default: 408).
 ```txt
  -S, -summary
 ```
-Write the analysis summary to this file. The summary is not
-reported unless a file is specified here. This option is correct as of v1.4.0.
+Write the analysis summary to this file. The summary is not reported
+unless a file is specified here. This option is correct as of v1.4.0.

docs/content/pmd.md

@@ -190,6 +190,5 @@ Specify a random seed value.
 ```txt
  -S, -summary
 ```
-Write the analysis summary to this file. The summary is not
-reported unless a file is specified here. This option is correct as of v1.4.0.
-
+Write the analysis summary to this file. The summary is not reported
+unless a file is specified here. This option is correct as of v1.4.0.

docs/content/selectsites.md

@@ -44,3 +44,18 @@ preload sites (use for large target intervals)
  -v, -verbose
 ```
 print more run info to STDERR while the program is running.
+
+```txt
+ -d, -disk
+```
+process sites on disk (fast if target intervals are few)
+
+```txt
+ -S, -summary
+```
+write summary to this file
+
+```txt
+ -z, -zip
+```
+output file will be in gzip compressed format

docs/content/states.md

@@ -69,4 +69,9 @@ FASTA file of chromosomes containing FASTA files [required].
 ```txt
  -v, -verbose
 ```
-Print more run info to STDERR while the program is running.
+Print information to the terminal while the program runs.
+
+```txt
+ -z, -zip
+```
+Write output in gzip compressed format.