[med-svn] [Git][med-team/fastp][upstream] New upstream version 0.20.1+dfsg
Dylan Aïssi
gitlab at salsa.debian.org
Sat Apr 11 21:16:43 BST 2020
Dylan Aïssi pushed to branch upstream at Debian Med / fastp
Commits:
fcc688de by Dylan Aïssi at 2020-04-11T22:14:24+02:00
New upstream version 0.20.1+dfsg
- - - - -
10 changed files:
- README.md
- src/common.h
- src/htmlreporter.cpp
- src/main.cpp
- src/options.cpp
- src/options.h
- src/peprocessor.cpp
- src/read.cpp
- src/read.h
- src/seprocessor.cpp
Changes:
=====================================
README.md
=====================================
@@ -304,7 +304,7 @@ options:
-I, --in2 read2 input file name (string [=])
-O, --out2 read2 output file name (string [=])
--unpaired1 for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. (string [=])
- --unpaired2 for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --umpaired1 (default mode), both unpaired reads will be written to this same file. (string [=])
+ --unpaired2 for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be written to this same file. (string [=])
--failed_out specify the file to store reads that cannot pass the filters. (string [=])
-m, --merge for paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.
--merged_out in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output (string [=])
@@ -316,6 +316,7 @@ options:
--interleaved_in indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default.
--reads_to_process specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])
--dont_overwrite don't overwrite existing files. Overwritting is allowed by default.
+ --fix_mgi_id the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.
# adapter trimming options
-A, --disable_adapter_trimming adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
=====================================
src/common.h
=====================================
@@ -1,7 +1,7 @@
#ifndef COMMON_H
#define COMMON_H
-#define FASTP_VER "0.20.0"
+#define FASTP_VER "0.20.1"
#define _DEBUG false
=====================================
src/htmlreporter.cpp
=====================================
@@ -406,7 +406,7 @@ void HtmlReporter::printCSS(ofstream& ofs){
}
void HtmlReporter::printJS(ofstream& ofs){
- ofs << "<script src='https://cdn.plot.ly/plotly-latest.min.js'></script>" << endl;
+ ofs << "<script src='http://opengene.org/plotly-1.2.0.min.js'></script>" << endl;
ofs << "\n<script type=\"text/javascript\">" << endl;
ofs << " function showOrHide(divname) {" << endl;
ofs << " div = document.getElementById(divname);" << endl;
=====================================
src/main.cpp
=====================================
@@ -36,7 +36,7 @@ int main(int argc, char* argv[]){
cmd.add<string>("in2", 'I', "read2 input file name", false, "");
cmd.add<string>("out2", 'O', "read2 output file name", false, "");
cmd.add<string>("unpaired1", 0, "for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it.", false, "");
- cmd.add<string>("unpaired2", 0, "for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --umpaired1 (default mode), both unpaired reads will be written to this same file.", false, "");
+ cmd.add<string>("unpaired2", 0, "for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be written to this same file.", false, "");
cmd.add<string>("failed_out", 0, "specify the file to store reads that cannot pass the filters.", false, "");
cmd.add("merge", 'm', "for paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.");
cmd.add<string>("merged_out", 0, "in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output", false, "");
@@ -48,6 +48,7 @@ int main(int argc, char* argv[]){
cmd.add("interleaved_in", 0, "indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default.");
cmd.add<int>("reads_to_process", 0, "specify how many reads/pairs to be processed. Default 0 means process all reads.", false, 0);
cmd.add("dont_overwrite", 0, "don't overwrite existing files. Overwritting is allowed by default.");
+ cmd.add("fix_mgi_id", 0, "the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.");
cmd.add("verbose", 'V', "output verbose log information (i.e. when every 1M reads are processed).");
// adapter
@@ -177,6 +178,7 @@ int main(int argc, char* argv[]){
opt.outputToSTDOUT = cmd.exist("stdout");
opt.interleavedInput = cmd.exist("interleaved_in");
opt.verbose = cmd.exist("verbose");
+ opt.fixMGI = cmd.exist("fix_mgi_id");
// merge PE
opt.merge.enabled = cmd.exist("merge");
=====================================
src/options.cpp
=====================================
@@ -26,6 +26,7 @@ Options::Options(){
verbose = false;
seqLen1 = 151;
seqLen2 = 151;
+ fixMGI = false;
}
void Options::init() {
=====================================
src/options.h
=====================================
@@ -325,6 +325,8 @@ public:
bool interleavedInput;
// only process first N reads
int readsToProcess;
+ // fix the MGI ID tailing issue
+ bool fixMGI;
// worker thread number
int thread;
// trimming options
=====================================
src/peprocessor.cpp
=====================================
@@ -338,6 +338,11 @@ bool PairEndProcessor::processPairEnd(ReadPairPack* pack, ThreadConfig* config){
continue;
}
+ // fix MGI
+ if(mOptions->fixMGI) {
+ or1->fixMGI();
+ or2->fixMGI();
+ }
// umi processing
if(mOptions->umi.enabled)
mUmiProcessor->process(or1, or2);
=====================================
src/read.cpp
=====================================
@@ -135,6 +135,17 @@ string Read::toStringWithTag(string tag) {
return mName + " " + tag + "\n" + mSeq.mStr + "\n" + mStrand + "\n" + mQuality + "\n";
}
+bool Read::fixMGI() {
+ int len = mName.length();
+ if(mName[len-1]=='1' || mName[len-1]=='2') {
+ if(mName[len-2] == '/') {
+ mName = mName.substr(0, len-2) + " " + mName.substr(len-2, 2);
+ return true;
+ }
+ }
+ return false;
+}
+
bool Read::test(){
Read r("@NS500713:64:HFKJJBGXY:1:11101:20469:1097 1:N:0:TATAGCCT+GGTCCCGA",
"CTCTTGGACTCTAACACTGTTTTTTCTTATGAAAACACAGGAGTGATGACTAGTTGAGTGCATTCTTATGAGACTCATAGTCATTCTATGATGTAGTTTTCCTTAGGAGGACATTTTTTACATGAAATTATTAACCTAAATAGAGTTGATC",
=====================================
src/read.h
=====================================
@@ -31,6 +31,7 @@ public:
void resize(int len);
void convertPhred64To33();
void trimFront(int len);
+ bool fixMGI();
public:
static bool test();
=====================================
src/seprocessor.cpp
=====================================
@@ -211,6 +211,11 @@ bool SingleEndProcessor::processSingleEnd(ReadPack* pack, ThreadConfig* config){
delete or1;
continue;
}
+
+ // fix MGI
+ if(mOptions->fixMGI) {
+ or1->fixMGI();
+ }
// umi processing
if(mOptions->umi.enabled)
View it on GitLab: https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755
--
View it on GitLab: https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755
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