modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 51fc0e7b3a93265eee63092adfe5ea75cdb87f6b..bf0ffa66009ba7cdc02f46ff4d2c784e58a45a1f 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -156,7 +156,7 @@ void ChimeraSeqsCommand::help(){
                mothurOut("The ksize parameter allows you to input kmersize. \n");
                mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence.\n");
                mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
-               mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n");
+               //mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n");
                mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
                mothurOut("Details for each method: \n"); 
                mothurOut("\tpintail: \n"); 
@@ -168,8 +168,8 @@ void ChimeraSeqsCommand::help(){
                mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n"); 
                mothurOut("\tchimeracheck: \n"); 
                mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n"); 
-               mothurOut("\tchimeraslayer: \n"); 
-               mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n"); 
+               //mothurOut("\tchimeraslayer: \n"); 
+               //mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n"); 
                mothurOut("The chimera.seqs command should be in the following format: \n");
                mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
                mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");