From 082883e98bd77139afa54868ca269fe3de49c3b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Armin=20To=CC=88pfer?= <atoepfer@pacificbiosciences.com>
Date: Mon, 9 Sep 2019 12:25:05 +0200
Subject: [PATCH] Version 1.10.0

   * Output N barcodes per subdirectory with `--files-per-directory N` and output splitting
   * BioSample awareness for XML input and split output and allow ignoring them with `--ignore-biosamples`
   * Increase `--window-size-mult` to `3` to allow longer spacers
   * Do not report no adapter hits as too short inserts
   * Increase `--guess` barcode score to `75` if `--peek-guess --ccs` are combined
   * Enable double demux of CCS data
   * Print run time, CPU time, and peak memory consumption with `--log-level INFO`
   * New CLI UX
---
 README.md | 40 +++++++++++++++++++++++++++++++++++++---
 1 file changed, 37 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 605578e..1bbaef0 100644
--- a/README.md
+++ b/README.md
@@ -115,7 +115,7 @@ to use `--no-pbi`, omit the pbi index file, to minimize time to result.
 
 ## Input data
 Input data is either raw unaligned subreads, straight from a Sequel, or
-unaligned CCS reads, generated by [CCS 2](https://github.com/PacificBiosciences/unanimity);
+unaligned CCS reads, generated by [CCS](https://github.com/PacificBiosciences/ccs);
 both in the PacBio enhanced BAM format. If you want to demux RSII data, first
 use SMRT Link or bax2bam to convert h5 to BAM. In addition, a `datastore.json`
 with one file entry, either a SubreadSet or ConsensusReadSet, is also allowed.
@@ -462,7 +462,7 @@ there is no way to distinguish between pairs `bc1001--bc1002` and `bc1002--bc100
 Score and tag per subread, instead per ZMW.
 
 ### `--window-size-mult`
-The candidate region size multiplier: `barcode_length * multiplier`, default `1.5`.
+The candidate region size multiplier: `barcode_length * multiplier`, default `3`.
 Optionally, you can specify the region size in base pairs with `--window-size-bp`.
 
 ### Alignment options
@@ -986,9 +986,43 @@ false positives.
  * Calls barcodes per barcode region and does not enforce adapter coupling
  * Nice reports for QC
 
+### Can I remove PCR primers after demultiplexing?
+Yes! After demultiplexing, just lima on the output again with your PCR primer(s).
+
+### Can I limit the output files per directory?
+If you use output BAM splitting, it can happen that you get a lot of output files.
+Using `--files-per-directory N` creates subdirectories and outputs at most `N`
+barcodes per directory.
+
+### `--peek-guess` does not work with XML input!
+If your input XML file contains `<BioSamples>`, lima will deactivate barcode
+inference via `--peek-guess` and only output barcodes specified in this section.
+The assumption is that you know exactly which barcodes have been used and need no
+inference. If this assumption is wrong, like the barcodes in the XML are wrong,
+you can either just use BAM as input or use `--ignore-biosamples`.
+
+### Help, I get `ERROR: Could not find matching barcodes!`
+If you happen to get following error message
+
+    ERROR: Could not find matching barcodes! Check that the set of barcodes contains the used sequences and the correct mode has been selected: same or different.
+
+then your XML input contains BioSamples with different barcode names than the
+provided `barcode.fasta` file. Please check that you've used the correct
+barcodes. You can ignore barcodes specified in the XML with `--ignore-biosamples`.
+
+
 ## Full Changelog
 
- * **1.9.0**:
+ * **1.10.0**:
+   * Output N barcodes per subdirectory with `--files-per-directory N` and output splitting
+   * BioSample awareness for XML input and split output and allow ignoring them with `--ignore-biosamples`
+   * Increase `--window-size-mult` to `3` to allow longer spacers
+   * Do not report no adapter hits as too short inserts
+   * Increase `--guess` barcode score to `75` if `--peek-guess --ccs` are combined
+   * Enable double demux of CCS data
+   * Print run time, CPU time, and peak memory consumption with `--log-level INFO`
+   * New CLI UX
+ * 1.9.0:
    * Add `--bad-adapter-ratio` to remove ZMWs with molecularly missing adapters
    * Fix rare case, where a read only matches one barcode and not a single alternative
    * Fix `--no-bam` to automatically omit pbi