From d39c47623faf0dc1e271f3d50efa6b029b622b88 Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Wed, 29 May 2013 14:16:43 -0400
Subject: [PATCH] get.seqs not renaming sequences correctly for dups=f.
unique.seqs crash when count table had group data.
---
clusterfragmentscommand.cpp | 2 +-
createdatabasecommand.cpp | 4 ++--
deconvolutecommand.cpp | 2 +-
getseqscommand.cpp | 8 ++++++--
makefile | 4 ++--
screenseqscommand.cpp | 6 +++---
6 files changed, 15 insertions(+), 11 deletions(-)
diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index f17c11e..9c1408c 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -181,7 +181,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
- else { ct.readTable(countfile, false); m->setCountTableFile(countfile); }
+ else { ct.readTable(countfile, true); m->setCountTableFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
diff --git a/createdatabasecommand.cpp b/createdatabasecommand.cpp
index 58799e7..5296279 100644
--- a/createdatabasecommand.cpp
+++ b/createdatabasecommand.cpp
@@ -380,8 +380,8 @@ int CreateDatabaseCommand::execute(){
if (countfile == "") {
sort(binNames.begin(), binNames.end());
bin = "";
- for (int i = 0; i < binNames.size()-1; i++) {
- bin += binNames[i] + ',';
+ for (int j = 0; j < binNames.size()-1; j++) {
+ bin += binNames[j] + ',';
}
bin += binNames[binNames.size()-1];
map<string, string>::iterator it = repNames.find(bin);
diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 8b73425..51fa43b 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -209,7 +209,7 @@ int DeconvoluteCommand::execute() {
}
CountTable ct;
if (countfile != "") {
- ct.readTable(countfile, false);
+ ct.readTable(countfile, true);
if (countfile == outCountFile){
//prepare filenames and open files
map<string, string> mvariables;
diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 9538698..83fdf73 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -430,9 +430,11 @@ int GetSeqsCommand::readFasta(){
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
- if (it != uniqueMap.end()) { name = it->second; }
+ if (it != uniqueMap.end()) { currSeq.setName(it->second); }
}
+ name = currSeq.getName();
+
if (name != "") {
//if this name is in the accnos file
if (names.count(name) != 0) {
@@ -710,7 +712,7 @@ int GetSeqsCommand::readName(){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> firstCol;
+ in >> firstCol; m->gobble(in);
in >> secondCol;
string hold = "";
@@ -734,6 +736,7 @@ int GetSeqsCommand::readName(){
selectedCount += parsedNames.size();
if (m->debug) { sanity["name"].insert(firstCol); }
}else {
+
selectedCount += validSecond.size();
//if the name in the first column is in the set then print it and any other names in second column also in set
@@ -752,6 +755,7 @@ int GetSeqsCommand::readName(){
//make first name in set you come to first column and then add the remaining names to second column
}else {
+
//you want part of this row
if (validSecond.size() != 0) {
diff --git a/makefile b/makefile
index 25ef4d4..163db6b 100644
--- a/makefile
+++ b/makefile
@@ -15,8 +15,8 @@ USEREADLINE ?= yes
CYGWIN_BUILD ?= no
USECOMPRESSION ?= no
MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"5/28/2013\""
-VERSION = "\"1.31.0\""
+RELEASE_DATE = "\"5/29/2013\""
+VERSION = "\"1.31.1\""
FORTAN_COMPILER = gfortran
FORTRAN_FLAGS =
diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 1d7cb8d..e7b2c6a 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -1820,7 +1820,6 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
vector<int> longHomoPolymer;
vector<int> numNs;
- vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
@@ -1845,8 +1844,9 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
- if (pid == 0) {
- driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]);
+ if (pid == 0) {
+ linePair tempLine(0, positions[positions.size()-1]);
+ driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, tempLine);
#else
int numSeqs = 0;
//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
--
2.39.5