Merge pull request #44 from pdimens/docs_dev

add bc threshold diagram

commonoptions.md

@@ -31,6 +31,7 @@ harpy align bwa --threads 20 --directory samples/trimmedreads --quiet
 
 harpy align bwa -t 20 -d samples/trimmedreads -q
 ```
+---
 
 ## The `workflow` folder
 When you run one of the main Harpy modules, the output directory will contain a `workflow` folder. This folder is
@@ -45,6 +46,8 @@ and the contents therein also allow you to rerun the workflow manually. The `wor
 | `report/*.Rmd` | RMarkdown files used to generate the fancy reports | useful to understand math behind plots/tables or borrow code from |
 | `*.workflow.summary` | Plain-text overview of the important parts of the workflow | useful for bookkeeping and writing Methods |
 
+---
+
 ## The `Genome` folder
 
 You will notice that many of the workflows will create a `Genome` folder in the working 

haplotagdata.md

@@ -83,4 +83,11 @@ same barcode (on the same contig), then we'll consider them as originating from
 you are being more strict and indicating that alignments sharing barcodes must be closer together to be considered originating from the same
 DNA molecule. Conversely, a higher threshold indicates you are being more lax and indicating barcodes can be further away from each other
 and still be considered originating from the same DNA molecule. A threshold of 50kb-150kb is considered a decent balance, but you should choose
-larger/smaller values if you have evidence to support them. 
+larger/smaller values if you have evidence to support them. 
+
+![Molecule origin is determined by the distance between alignments with the same barcode relative to the specified threshold](/static/bc_threshold.png)
+
+| Alignment distance     |    Inferred origin  |
+|:-----------------------|:--------------------|
+| less than threshold    |     same molecule   |
+| greater than threshold | different molecules |