Merge pull request #14 from HKU-BAL/v0.1-r2

V0.1 r2

Author: zhengzhenxian

README.md

@@ -99,7 +99,7 @@ A pre-built docker image is available [here](https://hub.docker.com/layers/hkuba
 INPUT_DIR="[YOUR_INPUT_FOLDER]"        # e.g. /home/user1/input (absolute path needed)
 OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"      # e.g. /home/user1/output (absolute path needed)
 THREADS="[MAXIMUM_THREADS]"            # e.g. 8
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 docker run -it \
   -v ${INPUT_DIR}:${INPUT_DIR} \
@@ -124,14 +124,14 @@ Check [Usage](#Usage) for more options.
 INPUT_DIR="[YOUR_INPUT_FOLDER]"        # e.g. /home/user1/input (absolute path needed)
 OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"      # e.g. /home/user1/output (absolute path needed)
 THREADS="[MAXIMUM_THREADS]"            # e.g. 8
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 conda config --add channels defaults
 conda create -n singularity-env -c conda-forge singularity -y
 conda activate singularity-env
 
 # singularity pull docker pre-built image
-singularity pull docker://hkubal/clair3:v0.1-r1
+singularity pull docker://hkubal/clair3:v0.1-r2
 
 # run clair3 like this afterward
 singularity exec clair3_"${BIN_VERSION}".sif \
@@ -292,7 +292,7 @@ CONTIGS_LIST="[YOUR_CONTIGS_LIST]"     # e.g "chr21" or "chr21,chr22"
 INPUT_DIR="[YOUR_INPUT_FOLDER]"        # e.g. /home/user1/input  (absolute path needed)
 OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"      # e.g. /home/user1/output (absolute path needed)
 THREADS="[MAXIMUM_THREADS]"            # e.g. 8
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 docker run -it \
   -v ${INPUT_DIR}:${INPUT_DIR} \
@@ -315,7 +315,7 @@ KNOWN_VARIANTS_VCF="[YOUR_VCF_PATH]"   # e.g. /home/user1/known_variants.vcf.gz
 INPUT_DIR="[YOUR_INPUT_FOLDER]"        # e.g. /home/user1/input (absolute path needed)
 OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"      # e.g. /home/user1/output (absolute path needed)
 THREADS="[MAXIMUM_THREADS]"            # e.g. 8
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 docker run -it \
   -v ${INPUT_DIR}:${INPUT_DIR} \
@@ -350,7 +350,7 @@ BED_FILE_PATH="[YOUR_BED_FILE]"        # e.g. /home/user1/tmp.bed (absolute path
 INPUT_DIR="[YOUR_INPUT_FOLDER]"        # e.g. /home/user1/input (absolute path needed)
 OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"      # e.g. /home/user1/output (absolute path needed)
 THREADS="[MAXIMUM_THREADS]"            # e.g. 8
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 docker run -it \
   -v ${INPUT_DIR}:${INPUT_DIR} \
@@ -372,7 +372,7 @@ docker run -it \
 INPUT_DIR="[YOUR_INPUT_FOLDER]"        # e.g. /home/user1/input (absolute path needed)
 OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"      # e.g. /home/user1/output (absolute path needed)
 THREADS="[MAXIMUM_THREADS]"            # e.g. 8
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 docker run -it \
   -v ${INPUT_DIR}:${INPUT_DIR} \

clair3/CallVariants.py

@@ -18,7 +18,7 @@
 )
 import clair3.utils as utils
 from clair3.task.genotype import Genotype, genotype_string_from, genotype_enum_from, genotype_enum_for_task
-from shared.utils import IUPAC_base_to_ACGT_base_dict as BASE2ACGT, BASIC_BASES, str2bool
+from shared.utils import IUPAC_base_to_ACGT_base_dict as BASE2ACGT, BASIC_BASES, str2bool, file_path_from
 from clair3.task.variant_length import VariantLength
 
 os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
@@ -265,7 +265,7 @@ def output_header():
                       ))
 
         if reference_file_path is not None:
-            reference_index_file_path = reference_file_path + ".fai"
+            reference_index_file_path = file_path_from(reference_file_path, suffix=".fai", exit_on_not_found=True, sep='.')
             with open(reference_index_file_path, "r") as fai_fp:
                 for row in fai_fp:
                     columns = row.strip().split("\t")

docs/quick_demo/illumina_quick_demo.md

@@ -49,7 +49,7 @@ echo -e "${CONTIGS}\t${START_POS}\t${END_POS}" > ${INPUT_DIR}/quick_demo.bed
 ### Option 1. Docker pre-built image
 
 ```bash
-BIN_VERSION='v0.1-r1'
+BIN_VERSION='v0.1-r2'
 THREADS=4
 cd ${OUTPUT_DIR}
 

docs/quick_demo/ont_quick_demo.md

@@ -49,7 +49,7 @@ echo -e "${CONTIGS}\t${START_POS}\t${END_POS}" > ${INPUT_DIR}/quick_demo.bed
 
 ```bash
 THREADS=4
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 cd ${OUTPUT_DIR}
 # Run Clair3 using one command

docs/quick_demo/pacbio_hifi_quick_demo.md

@@ -50,7 +50,7 @@ echo -e "${CONTIGS}\t${START_POS}\t${END_POS}" > ${INPUT_DIR}/quick_demo.bed
 
 ```bash
 THREADS=4
-BIN_VERSION="v0.1-r1"
+BIN_VERSION="v0.1-r2"
 
 cd ${OUTPUT_DIR}
 # Run Clair3 using one command