Merge pull request #142 from NuttyLogic/dev

MethylDackel support, Output to stdout option
NuttyLogic · Mar 27, 2023 · 85f4225 · 85f4225
2 parents 7d44bea + 388f4cf
commit 85f4225
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diff --git a/README.md b/README.md
@@ -22,6 +22,9 @@ doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5
 Documentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/).
 
 ## Release Notes
+- v1.6.0
+  - MethyDackel compatibility 
+  - Option to output alignment to stdout
 - v1.5.0
   - Improved thread handling for methylation / variant calling.
   - Experimental bisulfite aware SNP caller. 

diff --git a/docs/align.md b/docs/align.md
@@ -33,6 +33,7 @@ Input / Output Options:
   -F1 File     path to fastq 1
   -F2 File     path to fastq 2 [null]
   -O File      output Prefix
+  -OS          output to stdout [False]
   -OT Int      number of bam output threads [1]
   -DB File     path to bsbolt database
   -R Str       read group header line such as '@RG ID:foo SM:bar' [null]

diff --git a/docs/alignment_output.md b/docs/alignment_output.md
@@ -16,7 +16,8 @@ will always be assigned a mapping quality of zero.
 |XB    |Z (string)| Read bisulfite conversion position and context | 5zz1x3z11zZ15z8zZ6z2z11z3xz3z13Xz2|
 |XC    |i (int)| Bisulfite conversion status, 1 if not fully converted, 0 if converted | XC:i:0|  
 |YC    |i (integer)| Bisulfite ambiguous, 1 if ambiguous, not reported if non-ambiguous| YC:i:1 |
-|YS    |Z (string)| Mapping strand (C=Crick, W=Watson) and alignment conversion pattern (C2T or G2A) | YS:Z:W_C2T (ie. Watson_Cytosine.to.Thymine)|  
+|YS    |Z (string)| Mapping strand (C=Crick, W=Watson) and alignment conversion pattern (C2T or G2A) | YS:Z:W_C2T (ie. Watson_Cytosine.to.Thymine)|
+|XG | Z (string) | Mapping strand for MethylDackel compatibility (Crick=GA, Watson=CT)| XG:Z:CT |
 
 ### **MD and XB Tags**
 

diff --git a/docs/index.md b/docs/index.md
@@ -18,6 +18,12 @@ BSBolt is released under the MIT license.
 doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610)
 
 ## Release Notes
+- v1.6.0
+  - MethyDackel compatibility 
+  - Option to output alignment to stdout
+- v1.5.0
+  - Improved thread handling for methylation / variant calling.
+  - Experimental bisulfite aware SNP caller. 
 - v1.4.8
     - Fixed bug ending alignment when the reference template end greater than reference boundary.
 - v1.4.7

diff --git a/docs/variant_api.md b/docs/variant_api.md
@@ -0,0 +1,15 @@
+::: bsbolt.Variant.CallVariants
+    :docstring:
+    :members:
+
+::: bsbolt.Variant.BayesVariant
+    :docstring:
+    :members:
+
+::: bsbolt.Variant.ProcessVariantRegions
+    :docstring:
+    :members:
+
+::: bsbolt.Variant.VariantCall
+    :docstring:
+    :members:
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -29,6 +29,7 @@ nav:
     - Imputation: imputation_api.md
     - Simulation: simulation_api.md
     - Utilities: utils_api.md
+    - Variant Calling: variant_api.md
   #- Tutorial: tutorial.md
   #- Pipelines: pipelines.md