From a5b512626a7b8b5ee8f1ea70fe1b2e23c5e6bb05 Mon Sep 17 00:00:00 2001
From: hxj5 <hxj5@hku.hk>
Date: Thu, 23 Feb 2023 15:04:40 +0800
Subject: [PATCH] update to v1.2.3

---
 configure.ac    |  2 +-
 doc/conf.py     |  2 +-
 doc/manual.rst  | 11 ++++++++---
 doc/release.rst | 11 +++++++++++
 src/config.h    |  2 +-
 5 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/configure.ac b/configure.ac
index cf8a034..43989c4 100644
--- a/configure.ac
+++ b/configure.ac
@@ -7,7 +7,7 @@ dnl - github:htslib https://github.com/samtools/htslib/blob/550c6b1b98414ef60eeb
 dnl - github:samtools https://github.com/samtools/samtools/blob/develop/configure.ac
 
 AC_PREREQ([2.63])
-AC_INIT([cellsnp-lite], [1.2.2], [hxj5@hku.hk])
+AC_INIT([cellsnp-lite], [1.2.3], [hxj5@hku.hk])
 
 dnl Use subdir-objects option so that the source files in subdir `src`
 dnl could be compiled successfully
diff --git a/doc/conf.py b/doc/conf.py
index 0e3f3bc..2d182d0 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -22,7 +22,7 @@
 author = 'Xianjie Huang'
 
 # The full version, including alpha/beta/rc tags
-release = 'v1.2.2'
+release = 'v1.2.3'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/doc/manual.rst b/doc/manual.rst
index 8b7536b..967d115 100644
--- a/doc/manual.rst
+++ b/doc/manual.rst
@@ -138,7 +138,7 @@ version you are using):
 
 .. code-block:: html
 
-  Version: 1.2.2 (htslib 1.11-79-g53d7277)
+  Version: 1.2.3 (htslib 1.11-79-g53d7277)
   Usage:   cellsnp-lite [options]
   
   Options:
@@ -168,7 +168,7 @@ version you are using):
                          missing REFs in the input VCF for Mode 1.
     --chrom STR          The chromosomes to use, comma separated [1 to 22]
     --cellTAG STR        Tag for cell barcodes, turn off with None [CB]
-    --UMItag STR         Tag for UMI: UR, Auto, None. For Auto mode, use UR if barcodes are inputted,
+    --UMItag STR         Tag for UMI: UB, Auto, None. For Auto mode, use UB if barcodes are inputted,
                          otherwise use None. None mode means no UMI but read counts [Auto]
     --minCOUNT INT       Minimum aggragated count [20]
     --minMAF FLOAT       Minimum minor allele frequency [0.00]
@@ -180,7 +180,10 @@ version you are using):
                          (when use UMI) or UNMAP,SECONDARY,QCFAIL,DUP (otherwise)]
     --minLEN INT         Minimum mapped length for read filtering [30]
     --minMAPQ INT        Minimum MAPQ for read filtering [20]
-    --maxDEPTH INT       Maximum depth for one site of one file; 0 means highest possible value [0]
+    --maxPILEUP INT      Maximum pileup for one site of one file (including those filtered reads),
+                         avoids excessive memory usage; 0 means highest possible value [0]
+    --maxDEPTH INT       Maximum depth for one site of one file (excluding those filtered reads),
+                         avoids excessive memory usage; 0 means highest possible value [0]
     --countORPHAN        If use, do not skip anomalous read pairs.
   
   Note that the "--maxFLAG" option is now deprecated, please use "--inclFLAG" or "--exclFLAG"
@@ -204,6 +207,8 @@ Some Details:
 Notes
 -----
 
+Since v1.2.3, ``UB``, instead of ``UR``, is used as default UMI tag when barcodes are given.
+
 The ``Too many open files`` issue has been fixed (since v1.2.0). The issue is commonly
 caused by exceeding the `RLIMIT_NOFILE`_ resource limit (ie. the max number of files allowed
 to be opened by system for single process), which is typically 1024. Specifically, in the
diff --git a/doc/release.rst b/doc/release.rst
index 1cc36c6..b7ae2c1 100644
--- a/doc/release.rst
+++ b/doc/release.rst
@@ -2,6 +2,17 @@
 History
 =======
 
+Release v1.2.3 (23/02/2023)
+===========================
+* use UB instead of UR as default UMI tag when barcodes are given.
+* add --maxPILEUP and update --maxDEPTH.
+* fix the segmentation fault of getopt_long when given unrecognized 
+  cmdline parameters.
+* allow more cmdline options in lower case.
+* print CMD, VERSION and global settings.
+* improve logging output.
+* update manual according to issues (till Feb 23, 2023).
+
 Release v1.2.2 (03/11/2021)
 ===========================
 * add -f/--refseq so that the real (genomic) ref could be extracted from
diff --git a/src/config.h b/src/config.h
index f926935..78fe4c9 100644
--- a/src/config.h
+++ b/src/config.h
@@ -10,7 +10,7 @@
 #define DEVELOP 0
 
 #define CSP_NAME "cellsnp-lite"
-#define CSP_VERSION "1.2.2"
+#define CSP_VERSION "1.2.3"
 #define CSP_AUTHOR "hxj5<hxj5@hku.hk>"
 
 #define JF_ZIP_TYPE         2  // 1, gzip; 2, bgzip.