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FastDup
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Merge branch 'main' of https://github.com/zzhofict/FastDup

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zzh 2025-04-23 15:02:54 +08:00
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README.md
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@ -2,8 +2,7 @@
Identifies duplicate reads. This tool locates and tags duplicate reads in a coordinate ordered SAM or BAM file.
Use the same algorithm as picard MarkDuplicates and output identical results.
Use spdlog as log tool and the default level is 'info'.
Use the same algorithm as picard MarkDuplicates and output identical results, and use spdlog as log tool and the default level is 'info'.
### Features
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## Requirements
### Build tools
Install following tools and required libraries.
* autoconf (for htslib)
* cmake
* c++17 (gcc >= 8.1 or clang >= 7 should work.)
### Libraries needed
* zlib
* libbz2
* liblzma
* libcurl
* OpenSSL
* libdeflate (optional)
```bash
# install autoconf (for htslib), cmake, c++17 (gcc >= 8.1 or clang >= 7 should work), zlib, libbz2, liblzma, libcurl, libdeflate (optional)
sudo apt update
sudo apt install autoconf cmake g++-8 zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libdeflate-dev gcc-8 g++-8
```
## Install
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## Usage
1. get help
Get help
```bash
./fastdup --help
```
2. mark duplicates on an input BAM file using 8 threads
Mark duplicates on an input BAM file using 8 threads
```bash
./fastdup --input in_test.bam --output out_md.bam --metrics stats.txt --num-threads 8