[med-svn] [Git][med-team/mothur][master] 3 commits: update std-ver to 4.7.4 and debhelper 14
Tomasz Buchert (@tomasz)
gitlab at salsa.debian.org
Sat Aug 1 13:59:01 BST 2026
Tomasz Buchert pushed to branch master at Debian Med / mothur
Commits:
191cfc1e by Tomasz Buchert at 2026-08-01T14:39:08+02:00
update std-ver to 4.7.4 and debhelper 14
- - - - -
00ef2cb5 by Tomasz Buchert at 2026-08-01T14:58:33+02:00
New upstream version 1.48.6
- - - - -
db9594a6 by Tomasz Buchert at 2026-08-01T14:58:33+02:00
release
- - - - -
4 changed files:
- debian/changelog
- debian/control
- source/commands/chimeravsearchcommand.cpp
- source/commands/pcrseqscommand.cpp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+mothur (1.48.6-1) unstable; urgency=medium
+
+ * New upstream version 1.48.6
+ * Update std-ver to 4.7.4 and debhelper 14
+
+ -- Tomasz Buchert <tomasz at debian.org> Sat, 01 Aug 2026 14:43:04 +0200
+
mothur (1.48.5-2) unstable; urgency=medium
* Fix hardening flags for uchime
=====================================
debian/control
=====================================
@@ -1,12 +1,12 @@
Source: mothur
-Standards-Version: 4.7.3
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Tomasz Buchert <tomasz at debian.org>
Section: science
-Build-Depends: debhelper (>= 13),
- debhelper-compat (= 13),
+Build-Depends: debhelper-compat (= 14),
+ dh-sequence-single-binary,
gfortran,
libboost-iostreams-dev,
libreadline-dev,
=====================================
source/commands/chimeravsearchcommand.cpp
=====================================
@@ -407,14 +407,14 @@ void driver(vsearchData* params){
#endif
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: vsearch command = " + commandString + ".\n"); }
-
+
system(commandString.c_str());
//free memory
for(int i = 0; i < cPara.size(); i++) { delete cPara[i]; }
delete[] vsearchParameters;
- if (fileToRemove != "") { params->util.mothurRemove(fileToRemove); }
+ if (!params->m->getDebug() && fileToRemove != "") { params->util.mothurRemove(fileToRemove); }
//remove "" from filenames
params->driverOutputFName = params->driverOutputFName.substr(1, params->driverOutputFName.length()-2);
=====================================
source/commands/pcrseqscommand.cpp
=====================================
@@ -244,12 +244,15 @@ int PcrSeqsCommand::execute(){
//don't write or keep if blank
bool wroteAccnos = false;
if (badNames.size() != 0) { writeAccnos(badNames, outputFileName); wroteAccnos = true; outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName); }
- else { m->mothurOut("[NOTE]: no sequences were bad, removing " + outputFileName + "\n\n"); }
+ else {
+ if (nomatch != "keep") {
+ m->mothurOut("[NOTE]: no sequences were bad, removing " + outputFileName + "\n\n"); }
+ }
if (util.isBlank(badSeqFile)) { util.mothurRemove(badSeqFile); }
else { outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile); }
- if (wroteAccnos) {
+ if (wroteAccnos && (nomatch != "keep")) {
string inputStringTemp = "";
if (countfile != "") { inputStringTemp += ", count=" + countfile; }
else{
@@ -552,10 +555,6 @@ bool trimStartEnd(Sequence& seq, pcrData* params) {
if ((seq.getStartPos() > params->start) || (seq.getEndPos() < params->end)) {
good = false;
- if (params->m->getDebug()) {
- params->m->mothurOut("[DEBUG]: " + seq.getName()+ " values at locations (" + toString(params->start) + "," + toString(params->end) + ") = (" + alignedString[params->start] + "," + alignedString[params->end] + ")\n");
-
- }
}
else {
if (params->end != -1) {
@@ -600,7 +599,6 @@ vector<string> trimPrimers(Sequence& seq, vector<TrimOligos*> trims, vector<int>
string trashCode = ""; string commentString = "";
int currentSeqsDiffs = 0; int reverseIndex = 0; int primerIndex = 0;
- bool goodSeq = true;
if(params->numFPrimers != 0){
int primerStart = 0; int primerEnd = 0;
@@ -610,7 +608,7 @@ vector<string> trimPrimers(Sequence& seq, vector<TrimOligos*> trims, vector<int>
currentSeqsDiffs += results[0];
commentString += "fpdiffs=" + toString(results[0]) + "(" + trims[i]->getCodeValue(results[1], params->pdiffs) + ") ";
- if(!good){ if (params->nomatch == "reject") { goodSeq = false; } trashCode += "f"; }
+ if(!good){ trashCode += "f"; }
else{
//are you aligned
if (aligned) {
@@ -649,7 +647,7 @@ vector<string> trimPrimers(Sequence& seq, vector<TrimOligos*> trims, vector<int>
currentSeqsDiffs += results[0];
commentString += "rpdiffs=" + toString(results[0]) + "(" + trims[i]->getCodeValue(results[1], params->rdiffs) + ") ";
- if(!good){ if (params->nomatch == "reject") { goodSeq = false; } trashCode += "r"; }
+ if(!good){ trashCode += "r"; }
else{
//are you aligned
if (aligned) {
@@ -753,7 +751,7 @@ int driverPcr(pcrData* params){
currSeq.setComment("\t" + commentString + "\t" + seqComment);
}
- if (trashCode != "") { goodSeq = false; }
+ if (trashCode != "") { if (params->nomatch == "reject") { goodSeq = false; } }
}else if (params->ecoli.getName() != "filler") {
//make sure the seqs are aligned
@@ -771,11 +769,17 @@ int driverPcr(pcrData* params){
}
}
}else{ //using start and end to trim
- goodSeq = trimStartEnd(currSeq, params); //error message if seqs unaligned
+ //error message if seqs unaligned
+ if (!trimStartEnd(currSeq, params)) {
+ if (params->nomatch == "reject") { goodSeq = false; }
+ }
}
//remove super short reads
- if (currSeq.getUnaligned() == "") { goodSeq = false; currSeq.setAligned("NNNNNNN"); }
+ if (currSeq.getUnaligned() == "") {
+ if (params->nomatch == "reject") { goodSeq = false; }
+ currSeq.setAligned("NNNNNNN");
+ }
if(goodSeq) {
currSeq.printSequence(params->goodFasta);
View it on GitLab: https://salsa.debian.org/med-team/mothur/-/compare/025eeade50438591959cf10ceb135052d43ec0ce...db9594a6beeca4fcf9a17e962cafc4315a0a766c
--
View it on GitLab: https://salsa.debian.org/med-team/mothur/-/compare/025eeade50438591959cf10ceb135052d43ec0ce...db9594a6beeca4fcf9a17e962cafc4315a0a766c
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