pie-phasing-benchmark 0.11.1__tar.gz

pie_phasing_benchmark-0.11.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Jun Mencius
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pie_phasing_benchmark-0.11.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: pie-phasing-benchmark
+Version: 0.11.1
+Summary: Phasing all-in-one evaluator
+Home-page: https://github.com/JMencius/pie
+Author: Jun Mencius
+Author-email: zjmeng22@m.fudan.edu.cn
+Keywords: pie,haplotype,phasing,benchmark
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click>=8.1.8
+Requires-Dist: cyvcf2>=0.31.3
+Requires-Dist: sortedcontainers>=2.4.0
+Requires-Dist: pyfastx>=2.2.0
+Requires-Dist: lmdb==1.8.1; python_version < "3.9"
+Requires-Dist: lmdb>=2.0.0; python_version >= "3.9"
+Requires-Dist: numba>=0.58.1
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+
+<img src="pie_logo.png" width = "100">  
+
+# pie
+Phasing all-In-one Evaluator, for haplotype phasing evaluation
+
+## Installation
+Currently, `Pie` does not support online installation, but will be available through `pip` or `conda` upon publication.
+
+Installation will finish in a few minutes.
+
+### Use `pip` to conduct local installation
+1. Create new virtual environment
+```
+conda create -n pie python=3.8;
+conda activate pie;
+```
+
+2. Navigate to the base directory, which contains `setup.py`. Use `pip` to install `pie`.
+```
+pip install .;
+```
+
+## Usages
+### Required arguments
+| Parameters | Description | Format or example |
+|:---:|:---:|:---:| 
+| `-i or --input` | file for evaluation | .vcf / .vcf.gz |
+| `-c or --compare` | ground truth file | .vcf / .vcf.gz |
+| `-r or --ref` | reference file | .fa / .fasta / .fai |
+| `-o or --output` | Output file prefix | exmaple: ./test/output_name |
+
+### Recommend flag
+Use `--verbose` to monitor the running process and enable detailed logging. 
+
+### Full usages
+```
+Usage: pie [OPTIONS]
+
+Options:
+  -i, --input TEXT       Input vcf/vcf.gz file for evaluation  [required]
+  -n, --name TEXT        User defined sample name, [default: Sample]
+  -c, --compare TEXT     Ground truth vcf/vcf.gz file for comparison
+                         [required]
+  -r, --ref TEXT         Reference file fasta file (.fasta or .fa) or fasta
+                         index file (.fai)  [required]
+  -o, --output TEXT      Output file prefix,  such as -o ./test/output_name
+                         [required]
+  -t, --threads INTEGER  Maximum numbers of parallel threads [default: 24]
+  -m, --max-len INTEGER  Maximum variant distance for pairwise calculation
+                         [default: 250000]
+  -b, --bed TEXT         .bed file specifying genomic regions to include
+                         [default: None]
+  --min-sv INTEGER       Minimal length threshold of Structral Variant
+                         [default: 30, ALT length > 30 bp is SV]
+  --chrom TEXT           Chromosome to evaluate,use comma to join chromosome
+                         name e.g. --chrom chr1,chr2,chr3
+                         [default:chr1,chr2,chr3,...,chr22]
+  --sexchrom TEXT        Sex chromosme,use comma to join chromosome name e.g.
+                         --sexchrom chrX,chrY [default: chrX,chrY]
+  --mincount INTEGER     Minimum numbers of phased sites in a phase block
+                         [default: 2]
+  --block                Output phasing block start and end positions in a BED
+                         file
+  --no-sex               Ignore sex chromosome
+  --canonical            Canonical mode, only evaluate single mutation SNV
+                         ignore double heterozygous site
+  --only-snv             Only evaluate single nucleotide variation
+  --only-indel           Only evaluate insertion and deletion
+  --only-sv              Only evaluate structural variant
+  --no-snv               Ignore single nucleotide variation
+  --no-indel             Ignore insertion and deletion
+  --no-sv                Ignore structural variant
+  --no-double            Ignore double heterozygous site
+  --no-sort              Do not sort chromosome or regions, directly use the
+                         input order
+  --verbose              Enable verbose mode, printing parameters and progress
+                         to standard output
+  --version              Show the version and exit.
+  --help                 Show this message and exit.
+```
+
+## Exmaples
+Suppose `phase.vcf` is the sample VCF file to be evaluated against the ground truth VCF file (`truth.vcf`).
+1. (Comprehensive) Evaluate all autosome
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa -o ./output/comprehensive
+```
+
+2. (Chromosome specific) Restrict evaluation to selected chromosome
+```
+pie --verbose --chrom chr6 -i phase.vcf -c truth.vcf -r ref.fa -o ./output/chr6
+```
+
+3. (Region specific) Focus only on regions defined in a BED file.
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --bed mhc.bed -o ./output/mhc
+```
+
+4. (Filter) Exclude structural variants (SV) from the analysis
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --no-sv -o ./output/no_sv
+```
+
+5. (More output) Output raw phasing block start and end positions to a BED file
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --block -o ./output/more
+```
+
+6. (Miscellaneous) Evaluate only SNVs on chromosome 6 and output raw block start and end positions to a BED file.
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --chrom chr6 --only-snv --block -o ./output/misc
+```
+
+## Test data
+Small query and truth test files are provided in [here](./tests) including three formats:
+| Filename | Format | Description |
+|:---:|:---:|:---:|
+| small_query.vcf | VCF | Uncompressed VCF |
+| small_query.vcf.gz | VCF.GZ | Compressed VCF |
+| small_query.bcf | BCF | Binary VCF |
+
+`small_truth.vcf` is provided as the truth.
+
+The `VCF` format follows regulations in <https://samtools.github.io/hts-specs/VCFv4.1.pdf>
+
+
+## Output file
+| Output suffix | Description | Condition |
+|:---:|:---:|:--:|
+| `.variant.stats.csv` | Genotype evaluation result and phased percentage | Always generated |
+| `.perchrom.csv` | Per chromosome phasing evaluation result | Always generated |
+| `.overall.csv` | Overall sample evaluation result | Always generated |
+| `.blocks.bed` | Raw phasing block start end in `-i` or `--input` file | with `--block` set |
+
+
+## Resouce consumption
+`Pie` is expected to completed evaluation within minutes with the default 24 threads on a stardard X86 platfrom.
+
+The actual performance may vary depending on factors such as size of `vcf`, I/O speed, memory speed, and CPU capabilities.
+
+
+## Acknowledgements
+`Pie` is dependent on the following libraries, we are grateful to all the developers/maintainers:
+- [click](https://github.com/pallets/click): Python command line
+- [cyvcf2](https://github.com/brentp/cyvcf2): VCF/BCF  processing
+- [pyfastx](https://github.com/lmdu/pyfastx): Reference FASTA processing
+- [numba](https://github.com/numba/numba): JIT accerleration
+- [sortedcontainers](https://github.com/grantjenks/python-sortedcontainers): Python Sorted Container Types
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

pie_phasing_benchmark-0.11.1/README.md

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+<img src="pie_logo.png" width = "100">  
+
+# pie
+Phasing all-In-one Evaluator, for haplotype phasing evaluation
+
+## Installation
+Currently, `Pie` does not support online installation, but will be available through `pip` or `conda` upon publication.
+
+Installation will finish in a few minutes.
+
+### Use `pip` to conduct local installation
+1. Create new virtual environment
+```
+conda create -n pie python=3.8;
+conda activate pie;
+```
+
+2. Navigate to the base directory, which contains `setup.py`. Use `pip` to install `pie`.
+```
+pip install .;
+```
+
+## Usages
+### Required arguments
+| Parameters | Description | Format or example |
+|:---:|:---:|:---:| 
+| `-i or --input` | file for evaluation | .vcf / .vcf.gz |
+| `-c or --compare` | ground truth file | .vcf / .vcf.gz |
+| `-r or --ref` | reference file | .fa / .fasta / .fai |
+| `-o or --output` | Output file prefix | exmaple: ./test/output_name |
+
+### Recommend flag
+Use `--verbose` to monitor the running process and enable detailed logging. 
+
+### Full usages
+```
+Usage: pie [OPTIONS]
+
+Options:
+  -i, --input TEXT       Input vcf/vcf.gz file for evaluation  [required]
+  -n, --name TEXT        User defined sample name, [default: Sample]
+  -c, --compare TEXT     Ground truth vcf/vcf.gz file for comparison
+                         [required]
+  -r, --ref TEXT         Reference file fasta file (.fasta or .fa) or fasta
+                         index file (.fai)  [required]
+  -o, --output TEXT      Output file prefix,  such as -o ./test/output_name
+                         [required]
+  -t, --threads INTEGER  Maximum numbers of parallel threads [default: 24]
+  -m, --max-len INTEGER  Maximum variant distance for pairwise calculation
+                         [default: 250000]
+  -b, --bed TEXT         .bed file specifying genomic regions to include
+                         [default: None]
+  --min-sv INTEGER       Minimal length threshold of Structral Variant
+                         [default: 30, ALT length > 30 bp is SV]
+  --chrom TEXT           Chromosome to evaluate,use comma to join chromosome
+                         name e.g. --chrom chr1,chr2,chr3
+                         [default:chr1,chr2,chr3,...,chr22]
+  --sexchrom TEXT        Sex chromosme,use comma to join chromosome name e.g.
+                         --sexchrom chrX,chrY [default: chrX,chrY]
+  --mincount INTEGER     Minimum numbers of phased sites in a phase block
+                         [default: 2]
+  --block                Output phasing block start and end positions in a BED
+                         file
+  --no-sex               Ignore sex chromosome
+  --canonical            Canonical mode, only evaluate single mutation SNV
+                         ignore double heterozygous site
+  --only-snv             Only evaluate single nucleotide variation
+  --only-indel           Only evaluate insertion and deletion
+  --only-sv              Only evaluate structural variant
+  --no-snv               Ignore single nucleotide variation
+  --no-indel             Ignore insertion and deletion
+  --no-sv                Ignore structural variant
+  --no-double            Ignore double heterozygous site
+  --no-sort              Do not sort chromosome or regions, directly use the
+                         input order
+  --verbose              Enable verbose mode, printing parameters and progress
+                         to standard output
+  --version              Show the version and exit.
+  --help                 Show this message and exit.
+```
+
+## Exmaples
+Suppose `phase.vcf` is the sample VCF file to be evaluated against the ground truth VCF file (`truth.vcf`).
+1. (Comprehensive) Evaluate all autosome
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa -o ./output/comprehensive
+```
+
+2. (Chromosome specific) Restrict evaluation to selected chromosome
+```
+pie --verbose --chrom chr6 -i phase.vcf -c truth.vcf -r ref.fa -o ./output/chr6
+```
+
+3. (Region specific) Focus only on regions defined in a BED file.
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --bed mhc.bed -o ./output/mhc
+```
+
+4. (Filter) Exclude structural variants (SV) from the analysis
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --no-sv -o ./output/no_sv
+```
+
+5. (More output) Output raw phasing block start and end positions to a BED file
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --block -o ./output/more
+```
+
+6. (Miscellaneous) Evaluate only SNVs on chromosome 6 and output raw block start and end positions to a BED file.
+```
+pie --verbose -i phase.vcf -c truth.vcf -r ref.fa --chrom chr6 --only-snv --block -o ./output/misc
+```
+
+## Test data
+Small query and truth test files are provided in [here](./tests) including three formats:
+| Filename | Format | Description |
+|:---:|:---:|:---:|
+| small_query.vcf | VCF | Uncompressed VCF |
+| small_query.vcf.gz | VCF.GZ | Compressed VCF |
+| small_query.bcf | BCF | Binary VCF |
+
+`small_truth.vcf` is provided as the truth.
+
+The `VCF` format follows regulations in <https://samtools.github.io/hts-specs/VCFv4.1.pdf>
+
+
+## Output file
+| Output suffix | Description | Condition |
+|:---:|:---:|:--:|
+| `.variant.stats.csv` | Genotype evaluation result and phased percentage | Always generated |
+| `.perchrom.csv` | Per chromosome phasing evaluation result | Always generated |
+| `.overall.csv` | Overall sample evaluation result | Always generated |
+| `.blocks.bed` | Raw phasing block start end in `-i` or `--input` file | with `--block` set |
+
+
+## Resouce consumption
+`Pie` is expected to completed evaluation within minutes with the default 24 threads on a stardard X86 platfrom.
+
+The actual performance may vary depending on factors such as size of `vcf`, I/O speed, memory speed, and CPU capabilities.
+
+
+## Acknowledgements
+`Pie` is dependent on the following libraries, we are grateful to all the developers/maintainers:
+- [click](https://github.com/pallets/click): Python command line
+- [cyvcf2](https://github.com/brentp/cyvcf2): VCF/BCF  processing
+- [pyfastx](https://github.com/lmdu/pyfastx): Reference FASTA processing
+- [numba](https://github.com/numba/numba): JIT accerleration
+- [sortedcontainers](https://github.com/grantjenks/python-sortedcontainers): Python Sorted Container Types
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

pie_phasing_benchmark-0.11.1/pie/pie/module/F1_related.py

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+import math
+
+
+def cal_precision(TP: int, FP: int) -> float:
+    denominator = TP + FP
+    
+    if denominator != 0:
+        precision = TP / denominator
+        return precision
+    else:
+        return math.nan
+
+
+def cal_recall(TP: int, FN: int) -> float:
+    denominator = TP + FN
+
+    if denominator != 0:
+        recall = TP / denominator
+        return recall
+    else:
+        return math.nan
+
+
+def cal_f1(precision: float, recall: float) -> float:
+    denominator = precision + recall
+    if (denominator != 0) and not(math.isnan(denominator)):
+        F1 = (2 * precision * recall) / denominator
+        return F1
+    else:
+        return math.nan
+
+
+def cal_all(TP: int, FP: int, FN: int) -> tuple:
+    precision = cal_precision(TP, FP)
+    recall = cal_recall(TP, FN)
+    f1 = cal_f1(precision, recall)
+
+    return (precision, recall, f1)
+

pie_phasing_benchmark-0.11.1/pie/pie/module/cal_NGx0.py

@@ -0,0 +1,14 @@
+def cal_NGx0(len_list: list, total_len: int, p: int) -> int:
+    total_len = int(total_len)
+    target = total_len * p / 100
+
+    if sum(len_list) < target:
+        return None
+
+    len_list.sort(reverse = True)    
+
+    cummulative = 0
+    for i in len_list:
+        cummulative += i
+        if cummulative >= target:
+            return i

pie_phasing_benchmark-0.11.1/pie/pie/module/cal_ref.py

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+import pyfastx
+import os
+import sys
+import logging
+
+
+def get_ref_len(ref: str, chrom: list) -> dict:
+    suffix = os.path.splitext(ref)[1]
+    if suffix == ".fa" or suffix == ".fasta":
+        length_dict = fasta_mode(ref, chrom)
+        return length_dict
+    elif suffix == ".fai":
+        length_dict = fai_mode(ref, chrom)
+        return length_dict
+    else:
+        logging.error("Invalid file suffix of the reference file, must be either .fasta/.fa or .fai")
+        raise ValueError("Invalid file suffix of the reference file")
+
+
+
+def fasta_mode(ref: str, chrom: list) -> dict:
+    chr_len = dict()
+    exist = set()
+    for name, seq in pyfastx.Fasta(ref, build_index = False):
+        if name in chrom:
+            chr_len[name] = len(seq)
+            exist.add(name)
+
+    if len(chr_len) == len(chrom):
+        return chr_len
+    else:
+        for i in chrom:
+            if i not in exist:
+                logging.warning(f"{i} not in reference file")
+        return chr_len
+
+
+
+def fai_mode(ref_fai: str, chrom: list) -> dict:
+    chr_len = dict()
+    exist = set()
+    with open(ref_fai, 'r') as f:
+        for line in f:
+            m = line.split()
+            if len(m) >= 2:
+                name = m[0]
+                if name in chrom:
+                    chr_len[name] = int(m[1])
+                    exist.add(name)
+
+    if len(chr_len) == len(chrom):
+        return chr_len
+    else:
+        for i in chrom:
+            if i not in exist:
+                logging.warning(f"{i} not in reference file")
+        return chr_len
+                
+
+
+
+

pie_phasing_benchmark-0.11.1/pie/pie/module/check_filters.py

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+import logging
+
+
+def check_filters(filters: dict) -> bool:
+    only_count = ([filters["only_snv"], filters["only_indel"], filters["only_sv"]]).count(True)
+    if only_count > 1:
+        logging.error("Only one of --only_snv, --only_indel, or --only_sv can be set at a time.")
+        return False
+        
+    if filters["only_snv"] and filters["no_snv"]:
+        logging.error("Can not set --only_snv and --no_snv simultaneously")
+        return False
+
+    if filters["only_indel"] and filters["no_indel"]:
+        logging.error("Can not set --only_indel and --no_indel simultaneously")
+        return False
+
+    if filters["only_sv"] and filters["no_sv"]:
+        logging.error("Can not set --only_sv and --no_sv simultaneously")
+        return False
+   
+    return True

pie_phasing_benchmark-0.11.1/pie/pie/module/cli.py

@@ -0,0 +1,114 @@
+import os
+import sys
+import click
+import math
+from pathlib import Path
+from pie.module.sort_chrom import sort_chrom
+import logging
+
+@click.command()
+@click.option("-i", "--input", required = True, type = str, help = "Input vcf/vcf.gz file for evaluation")
+@click.option("-n", "--name", default = "Sample", type = str, help = "User defined sample name, [default: Sample]")
+@click.option("-c", "--compare", required = True, type = str, help = "Ground truth vcf/vcf.gz file for comparison")
+@click.option("-r", "--ref", required = True, type = str, help = "Reference file fasta file (.fasta or .fa) or fasta index file (.fai)")
+@click.option("-o", "--output", required = True, type = str, help = "Output file prefix,  such as -o ./test/output_name")
+@click.option("-t", "--threads", default = 24, type = int, help = "Maximum numbers of parallel threads [default: 24]")
+@click.option("-m", "--max-len", default = 250 * 10**3, type = int, help = "Maximum variant distance for pairwise calculation [default: 250000]")
+@click.option("-b", "--bed", default = None, type = str, help = r".bed file specifying genomic regions to include [default: None]")
+@click.option("--min-sv", default = 30, type = int, help = "Minimal length threshold of Structral Variant [default: 30, ALT length > 30 bp is SV]")
+@click.option("--chrom", default = ','.join(["chr" + str(i) for i in range(1, 23)]), type = str, help = "Chromosome to evaluate,use comma to join chromosome name e.g. --chrom chr1,chr2,chr3 [default:chr1,chr2,chr3,...,chr22]")
+@click.option("--sexchrom", default = "chrX,chrY", type = str, help = "Sex chromosme,use comma to join chromosome name e.g. --sexchrom chrX,chrY [default: chrX,chrY]")
+@click.option("--mincount", default = 2, type = int, help = "Minimum numbers of phased sites in a phase block [default: 2]")
+@click.option("--block", is_flag = True, help = r"Output phasing block start and end positions in a BED file")
+@click.option("--no-sex", is_flag = True, help = "Ignore sex chromosome")
+@click.option("--canonical", is_flag = True, help = "Canonical mode, only evaluate single mutation SNV ignore double heterozygous site")
+@click.option("--only-snv", is_flag = True, help = "Only evaluate single nucleotide variation")
+@click.option("--only-indel", is_flag = True, help = "Only evaluate insertion and deletion")
+@click.option("--only-sv", is_flag = True, help = "Only evaluate structural variant")
+@click.option("--no-snv", is_flag = True, help = "Ignore single nucleotide variation")
+@click.option("--no-indel", is_flag = True, help = "Ignore insertion and deletion")
+@click.option("--no-sv", is_flag = True, help = "Ignore structural variant")
+@click.option("--no-double", is_flag = True, help = "Ignore double heterozygous site")
+@click.option("--no-sort", is_flag = True, help = "Do not sort chromosome or regions, directly use the input order")
+@click.option("--lmdb", is_flag = True, hidden = True, help = "Output intermediate hamming result as .lmdb file")
+@click.option("--verbose", is_flag = True, help = "Enable verbose mode, printing parameters and progress to standard output")
+@click.version_option(version="0.11.1", prog_name = r"Phasing all-in-one evaluator (pie), based on Python 3.7+")
+def cli(input, name, compare, ref, output, threads, max_len, bed, min_sv, chrom, sexchrom, mincount, canonical, block, no_sex, only_snv, only_indel, only_sv, no_snv, no_indel, no_sv, no_double, no_sort, lmdb, verbose) -> tuple:
+
+    # set logging
+    logging.basicConfig(level = logging.DEBUG, format = "%(asctime)s - %(levelname)s - %(message)s")
+
+    # clean parameters
+    input = os.path.abspath(input)
+    compare = os.path.abspath(compare)
+    ref = os.path.abspath(ref)
+    
+    if bed:
+        bed = os.path.abspath(bed)
+    
+    if canonical:
+        only_snv = True
+        no_double = True
+    
+
+    # check parameters
+    input_vcf = Path(input)
+    compare_vcf = Path(compare)
+    if not (input_vcf.suffix == ".vcf" or input_vcf.suffix == ".bcf" or (".gz" in input_vcf.suffixes and ".vcf" in input_vcf.suffixes)):
+        raise ValueError(r"-i or --input must be .vcf or .vcf.gz file. You provided a file with a different extension")
+    if not (compare_vcf.suffix == ".vcf" or compare_vcf.suffix == ".bcf" or (".gz" in compare_vcf.suffixes and ".vcf" in compare_vcf.suffixes)):
+        raise ValueError(r"-c or --compare must be .vcf or .vcf.gz file. You provided a file with a different extension")     
+
+    ref_file = Path(ref)
+    if not (ref_file.suffix == ".fa" or ref_file.suffix == ".fasta" or ref_file.suffix == ".fai"):
+        raise ValueError(r"-r or --ref must be .fa, .fasta, or .fai file. You provided a file with a different extension") 
+
+    if bed:
+        bed_file = Path(bed)
+        if not (bed_file.suffix == ".bed"):
+            raise ValueError(r"--bed must be .bed file. You provided a file with a different extension")
+
+    output_dir = os.path.dirname(output)
+    if not (os.path.exists(output_dir)):
+        raise ValueError(f"The output directory {output_dir} does not exist")
+    else:
+        if not os.path.isdir(output_dir):
+            raise ValueError(f"The output directory {output_dir} exists but is not a directory")        
+
+    if threads > os.cpu_count():
+        logging.warning(f"-t or --threads set threads exceed the system CPU thread count ({os.cpu_count()})")
+        
+
+    # process chromosome area
+    chrom = [i.strip() for i in chrom.split(',')]
+    if not chrom:
+        raise ValueError("-c or --chrom must be in comma joined string e.g. chr1,chr2,ch3")
+    
+    sexchrom = [i.strip() for i in sexchrom.split(',')]
+    if not chrom:
+        raise ValueError("--sexchrom must be in comma joined string e.g. chr1,chr2,ch3")
+
+    if no_sex:
+        clean_chrom = []
+        for i in chrom:
+            if i not in sexchrom:
+                clean_chrom.append(i)
+        chrom = clean_chrom
+    
+    # sort chromosome
+    if not no_sort:
+        chrom = sort_chrom(chrom)
+
+    # print parameters in verbose mode
+    if verbose:
+        ctx = click.get_current_context()
+        logging.info("Command parameters:")
+        for param in ctx.command.params:
+            param_name = param.name
+            if param_name != "version":
+                param_value = ctx.params[param_name]
+                logging.info(f"{param_name}: {param_value}")
+
+    return (input, name, compare, ref, output, threads, max_len, bed, min_sv, chrom, sexchrom, mincount, canonical, block, no_sex, only_snv, only_indel, only_sv, no_snv, no_indel, no_sv, no_double, no_sort, lmdb, verbose)
+
+