From feb0cb8793572f75a037075ed255f73ecef263e0 Mon Sep 17 00:00:00 2001
From: zhengzhenxian <920596906@qq.com>
Date: Sun, 7 Apr 2024 18:22:30 +0800
Subject: [PATCH] updated readme

---
 README.md     | 2 ++
 run_clair3.sh | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index c5dac15..69d1222 100644
--- a/README.md
+++ b/README.md
@@ -63,6 +63,8 @@ For somatic variant calling using tumor-only samples, please try [ClairS-TO](htt
 ----
 
 ## Latest Updates
+*v1.0.7 (Apr 7, 2024)* : 1. Added memory guards and test function on full-alignment C implement ([#286](https://github.com/HKU-BAL/Clair3/pull/286) by @[Chris Wright](https://github.com/cjw85)). 2. Increased the maximum mpileup read coverage to 2^20 to adapt high-coverage amplicon data ([#292](https://github.com/HKU-BAL/Clair3/pull/292) by @[Devon Ryan](https://github.com/dpryan79)). 3. Updated LongPhase to version 1.6.
+
 *v1.0.6 (Mar 15, 2024)* : 1. Fixed stack overflow issue when the read coverage is excessively high ([#282](https://github.com/HKU-BAL/Clair3/issues/282) by @[Chris Wright](https://github.com/cjw85), [#265](https://github.com/HKU-BAL/Clair3/issues/265) by @[ymcki](https://github.com/ymcki)). 2. Added reference caching for CRAM input ([#278](https://github.com/HKU-BAL/Clair3/pull/278) by @[Alex Leonard](https://github.com/ASLeonard), [#180](https://github.com/HKU-BAL/Clair3/issues/180) by @[bartcharbon](https://github.com/bartcharbon) and @[SamStudio8](https://github.com/SamStudio8)). 3. Fixed a bug that outputs RefCall calls when no variant is called by full-alignment model ([#271](https://github.com/HKU-BAL/Clair3/issues/271)). 4. Fixed a bug that variants below min coverage were still being called ([#262](https://github.com/HKU-BAL/Clair3/issues/262)). 5. Set `--min_snp_af` and `--min_indel_af` to 0.0 when `--vcf_fn` is provided ([#261](https://github.com/HKU-BAL/Clair3/issues/261)).
 
 *v1.0.5 (Dec 20, 2023)* : 1. Fixed the issue showing wrong multi-allelic AF when read coverage is excessively high ([#241](https://github.com/HKU-BAL/Clair3/issues/241)). 2. Added `--base_err` and `--gq_bin_size` options that can resolve the problem of having excessive GT ./. in GVCF output ([#220](https://github.com/HKU-BAL/Clair3/issues/220)). 3. Modified logs ([#231](https://github.com/HKU-BAL/Clair3/issues/231), [#225](https://github.com/HKU-BAL/Clair3/issues/225))
diff --git a/run_clair3.sh b/run_clair3.sh
index 9df4c6a..6aa6b81 100755
--- a/run_clair3.sh
+++ b/run_clair3.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 SCRIPT_NAME=$(basename "$0")
 SCRIPT_PATH=$(dirname $(readlink -f "$0"))
-VERSION='v1.0.6'
+VERSION='v1.0.7'
 Usage="Usage: ${SCRIPT_NAME} --bam_fn=BAM --ref_fn=REF --output=OUTPUT_DIR --threads=THREADS --platform=PLATFORM --model_path=MODEL_PREFIX [--bed_fn=BED] [options]"
 
 CMD="$0 $@"