diff --git a/README.md b/README.md
index bd8e6567..a7f4a639 100644
--- a/README.md
+++ b/README.md
@@ -104,6 +104,9 @@ The following comments refer to the filters that are explained in the FAQ above.
CCS below minimum RQ : 0 (0.00%) <- Predicted accuracy is below --min-rq (5)
Unknown error : 0 (0.00%) <- Rare implementation errors
+If run in `--by-strand` mode, rows may contain half ZMWs, as we account
+each strand as half a ZMW.
+
### What is the definition of a heteroduplex?
In general, whenever bases on one strand of the SMRTbell are not the
reverse complement of the other strand, as small as a single base `A` with a
@@ -201,7 +204,8 @@ cp /some/download/dir/model.json "${SMRT_CHEMISTRY_BUNDLE_DIR}"/arrow/
### How fast is CCS?
We tested CCS runtime using 1,000 ZMWs per length bin with exactly 10 passes.
-
+
+
#### How does that translate into time to result per SMRT Cell?
We will measure time to result for Sequel I and II CCS sequencing collections
@@ -274,6 +278,15 @@ Read name suffix indicates strand. Example:
m64011_190714_120746/14/ccs/rev
m64011_190714_120746/35/ccs/fwd
+How does `--by-strand` work? For each ZMW:
+ * Determine orientation of reads with respect to the one closest to the mean length
+ * Sort reads into two buckets, forward and reverse strands
+ * Treat each strand as an individual entity as we do with ZMWs
+ * Apply all filters per strand individually
+ * Create a draft for each strand
+ * Polish each strand
+ * Write out each polished strand consensus
+
### Is there a progress report?
Yes. With `--log-level INFO`, _ccs_ provides status to `stderr` every
`--refresh-rate seconds` (default 30):
@@ -315,10 +328,16 @@ and statically links GNU C Library v2.29 licensed under [LGPL](https://spdx.org/
Per LPGL 2.1 subsection 6c, you are entitled to request the complete
machine-readable work that uses glibc in object code.
+
## Changelog
- * **4.0.0**:
- * SMRT Link v8.0 release candidate
+ * **4.1.0**:
+ * Minor speed improvements
+ * Fix `--by-strand` logic, see more [here](#can-i-produce-one-consensus-sequence-for-each-strand-of-a-molecule)
+ * Allow vanilla `.xml` output without specifying dataset type
+ * Compute wall start/end for each output read (future basecaller functionality)
+ * 4.0.0:
+ * SMRT Link v8.0 release
* Speed improvements
* Removed support for legacy python Genomic Consensus, please use [gcpp](https://github.com/PacificBiosciences/gcpp)
* New command-line interface
diff --git a/img/runtime.png b/img/runtime.png
index 63492414..00768e30 100644
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