From ed89a2b878a98634ad5b3c605892d559a2d26336 Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Wed, 12 Apr 2017 15:53:29 +0800 Subject: [PATCH] better and more informative output --- src/common.h | 2 +- src/htmlreporter.cpp | 11 ++++++----- src/multihtmlreporter.cpp | 10 ++++++++++ src/mutation.cpp | 1 - src/pescanner.cpp | 5 +++++ src/sescanner.cpp | 5 +++++ 6 files changed, 27 insertions(+), 7 deletions(-) diff --git a/src/common.h b/src/common.h index 40fe41b..d0d5817 100644 --- a/src/common.h +++ b/src/common.h @@ -1,7 +1,7 @@ #ifndef COMMON_H #define COMMON_H -#define MUTSCAN_VER "1.11.0" +#define MUTSCAN_VER "1.11.1" typedef long int64; typedef unsigned long uint64; diff --git a/src/htmlreporter.cpp b/src/htmlreporter.cpp index 75d0ab2..490cfe8 100644 --- a/src/htmlreporter.cpp +++ b/src/htmlreporter.cpp @@ -30,12 +30,13 @@ void HtmlReporter::printHelper() { mFile << ""; mFile << "
Print
"; mFile << "

Helpful tips:

"; } diff --git a/src/multihtmlreporter.cpp b/src/multihtmlreporter.cpp index 7fe4496..de69bd9 100644 --- a/src/multihtmlreporter.cpp +++ b/src/multihtmlreporter.cpp @@ -64,12 +64,14 @@ void MultiHtmlReporter::printMainPage() { } void MultiHtmlReporter::printAllChromosomeLink(ofstream& file) { + bool found = false; map::iterator iter; file << ""; } void MultiHtmlReporter::printChrLink(ofstream& file, string chr) { + bool found = false; for(int m=0; m matches = mMutationMatches[m]; if(matches.size()>=GlobalSettings::minReadSupport) { + found = true; if(chr == mMutationList[m].mChr) { string filename = chr + "/" + to_string(m) + ".html"; file << "
  • " << mMutationList[m].mName; @@ -92,6 +99,9 @@ void MultiHtmlReporter::printChrLink(ofstream& file, string chr) { } } } + if(!found) { + file << "MutScan didn't find any mutation"; + } } void MultiHtmlReporter::printMutationHtml() { diff --git a/src/mutation.cpp b/src/mutation.cpp index fda1e8e..8fe0e65 100644 --- a/src/mutation.cpp +++ b/src/mutation.cpp @@ -263,7 +263,6 @@ vector Mutation::parseVcf(string vcfFile, string refFile) { int lengthDiff = abs((int)v.ref.length() - (int)v.alt.length()); if(lengthDiff>=1 && lengthDiff<=2 ) mut.setSmallIndel(true); - cerr << name << ", " << left << ", " << center << ", " << right << ", " << chrom << endl; mutations.push_back(mut); } if(mutations.size() <= 0){ diff --git a/src/pescanner.cpp b/src/pescanner.cpp index e6110ac..f3bfb86 100644 --- a/src/pescanner.cpp +++ b/src/pescanner.cpp @@ -282,9 +282,11 @@ void PairEndScanner::consumerTask() void PairEndScanner::textReport(vector& mutationList, vector *mutationMatches) { //output result + bool found = false; for(int i=0;i matches = mutationMatches[i]; if(matches.size()>=GlobalSettings::minReadSupport){ + found = true; cout<& mutationList, vector * } } } + if(found == false) { + cout << "MutScan didn't find any mutation" << endl; + } } void PairEndScanner::htmlReport(vector& mutationList, vector *mutationMatches) { diff --git a/src/sescanner.cpp b/src/sescanner.cpp index d761ae6..b0af699 100644 --- a/src/sescanner.cpp +++ b/src/sescanner.cpp @@ -254,9 +254,11 @@ void SingleEndScanner::consumerTask() void SingleEndScanner::textReport(vector& mutationList, vector *mutationMatches) { //output result + bool found = false; for(int i=0;i matches = mutationMatches[i]; if(matches.size()>=GlobalSettings::minReadSupport){ + found = true; cout<& mutationList, vector } } } + if(found == false) { + cout << "MutScan didn't find any mutation" << endl; + } } void SingleEndScanner::htmlReport(vector& mutationList, vector *mutationMatches) {