添加README内容
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README.md
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README.md
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### Features
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* Fast -
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* Fast - with the same number of threads `FastDup` is ~3.5X faster than GATK MarkDuplicatesSpark.
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And `FastDup` achives ~15X performance improvement than Picard MarkDuplicates.
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* Generate identical outputs compared to Picard MarkDuplicates.
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* The same detailed metrics data witch Picard MarkDuplicates.
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* All data processed in memory and low-memory footprint even for large input files.
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### Limitations
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* Although `FastDup` can detecte all the same duplicates as Picard MarkDuplicates. They may mark
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different reads as duplicates because the reads sort algorithm in Picard MarkDuplicates is unstable.
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Considering there are 2 reads(A, B and A is in front of B in file) in a duplicate group and they
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have the same score, Picard Markduplicates may mark A as duplicate because B may be in front of A
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after sorting. While `FastDup` use stable sort algorithm and always mark B as duplicate.
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* In optical duplicates detection, Picard Markduplicates use short (int16_t) as data type in parsing
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tile/region, x coordinate and y coordinate from a read name, which may data overflow as these integers
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may exceed the range of short type. `FastDup` fixes this bug. But for consistency with Picard Markduplicates,
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we keep this bug in source codes. Just change the data type in PhysicalLocation struct in read_ends.h file
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to fix this bug.
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* `FastDup` use the data characteristics in coordinate ordered SAM/BAM files to improve the performance of
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detecting duplicates, thus the input should be ordered by coordinate in advance.
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## Requirements
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### Build tools
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* cmake
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* c++17 (gcc >= 8.1 or clang >= 7 should work.)
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### Libraries need
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* zlib
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* libbz2
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* liblzma
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* libcurl
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* libdeflate (optional)
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## Install
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Download a distribution tarball `FastDup.tar.gz` or clone the source codes from github.
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```
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# build htslib
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cd FastDup/ext/htslib
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autoreconf -i
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./configure
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make
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# build FastDup
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cd FastDup
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mkdir build && cd build
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cmake .. -DCMAKE_BUILD_TYPE=Release
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make && sudo make install
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```
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metrics.txt
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metrics.txt
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## StringHeader
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# /home/zzh/work/ngs/FastDup/build/bin/fastdup --input /home/zzh/data/bam/normal_all.sam --output /home/zzh/data1/out.sam --metrics ./metrics.txt --num-threads 1 --create-index --index-format CSI --tag-duplicate-set-members
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## StringHeader
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# Started on: December 16, 2024 at 02:43:41 AM CST
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## METRICS
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LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
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normal 108919 66154888 117508 161395 67414 15058359 876584 0.227945 127582703
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## HISTOGRAM Double
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BIN CoverageMult
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1 1.010249
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2 1.611750
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3 1.969882
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4 2.183113
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5 2.310070
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6 2.385660
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7 2.430666
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8 2.457463
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9 2.473417
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10 2.482917
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11 2.488573
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12 2.491940
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13 2.493945
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14 2.495139
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15 2.495850
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16 2.496273
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17 2.496525
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18 2.496675
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19 2.496764
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@ -303,7 +303,7 @@ int MarkDuplicates() {
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bam_aux_append(bw->b, "PG", 'Z', nsgv::gMdArg.PROGRAM_RECORD_ID.size() + 1,
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(const uint8_t *)nsgv::gMdArg.PROGRAM_RECORD_ID.c_str());
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}
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#if 0
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#if 1
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if (sam_write1(nsgv::gOutBamFp, nsgv::gOutBamHeader, bw->b) < 0) {
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spdlog::error("failed writing sam record to \"{}\"", nsgv::gMdArg.OUTPUT_FILE.c_str());
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sam_close(nsgv::gOutBamFp);
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/*
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Description: Markduplicate需要用到的一些参数，读取命令行给的参数，并做一些初始化
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2023/10/27
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*/
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#include <cstring>
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#include <iostream>
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#include <sstream>
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#include <string>
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#include <vector>
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#include "md_args.h"
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using std::cout, std::endl;
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using std::ostringstream;
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using std::stod;
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using std::stoi;
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using std::stol;
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using std::string;
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using std::vector;
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using namespace nsmd;
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