Doc updates

Author: ctsa

CHANGELOG.md

@@ -1,8 +1,16 @@
+## v2.2.0 - 2023-04-14
+
+### Added
+- Added progress bar to bam processing step
+
+### Fixed
+- Clarified error message when an unmapped alignment file is input
+
 ## v2.1.1 - 2023-04-04
 
 ### Fixed
 - Fix parse error in MM/ML methylation tags
-  - An infrequent error occurred when a reverse-mapped read ends (in sequenced orientation) with a methylated C base
+  - An infrequent error occurred when a reverse-mapped read ends (in sequenced orientation) with a C base annotated by the MM tag
   - Fixes #41
 
 ## v2.1.0 - 2023-03-27

README.md

@@ -7,22 +7,22 @@ mapped HiFi reads.
 
 To use `aligned_bam_to_cpg_scores` download the latest release tarball compiled for 64-bit linux platforms on the 
 [github release channel](https://github.com/PacificBiosciences/pb-CpG-tools/releases/latest), then unpack the tar file.
-As an example, the v2.1.1 release can be obtained as follows:
+As an example, the v2.2.0 release can be obtained as follows:
 
-    wget https://github.com/PacificBiosciences/pb-CpG-tools/releases/download/v2.1.1/pb-CpG-tools-v2.1.1-x86_64-unknown-linux-gnu.tar.gz
-    tar -xzf pb-CpG-tools-v2.1.1-x86_64-unknown-linux-gnu.tar.gz
+    wget https://github.com/PacificBiosciences/pb-CpG-tools/releases/download/v2.2.0/pb-CpG-tools-v2.2.0-x86_64-unknown-linux-gnu.tar.gz
+    tar -xzf pb-CpG-tools-v2.2.0-x86_64-unknown-linux-gnu.tar.gz
 
     # Run help option to test binary and see latest usage details:
-    pb-CpG-tools-v2.1.1-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores --help
+    pb-CpG-tools-v2.2.0-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores --help
 
 `aligned_bam_to_cpg_scores` includes a number of ways to summarize site propabilities for 5mC methylation,
 detailed below.  The recommended default workflow will use the `model` pileup mode and `denovo` modsites mode.
 Continuing from the example above, the script below runs the tool on a mapped WGS bam for HG002:
 
-    pb-CpG-tools-v2.1.1-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores \
+    pb-CpG-tools-v2.2.0-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores \
       --bam HG002.hg38.pbmm2.bam \
       --output-prefix HG002.hg38.pbmm2 \
-      --model pb-CpG-tools-v2.1.1-x86_64-unknown-linux-gnu/models/pileup_calling_model.v1.tflite \
+      --model pb-CpG-tools-v2.2.0-x86_64-unknown-linux-gnu/models/pileup_calling_model.v1.tflite \
       --threads 8
 
 See the cmdline usage help for the full list of other commandline options: