Tweet
Place this near the top of param.cpp:
Code:
#include<stdlib.h>
-
-
No luck...I'm corresponding with the SOAP team, hopefully they will be able to help me through it. Thanks for the help jjcook
Code:g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3 -DDB_CHR -DREAD_60 -c param.cpp -o param.chr.o g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3 -DDB_CHR -DREAD_60 -c reads.cpp -o reads.chr.o reads.cpp: In member function ‘void ReadClass::CheckFile(std::ifstream&)’: reads.cpp:32: error: ‘exit’ was not declared in this scope reads.cpp:37: error: ‘exit’ was not declared in this scope reads.cpp:41: error: ‘exit’ was not declared in this scope make: *** [reads.chr.o] Error 1
Comment
-
-
1.11 has solved all my compiling problems. Now to find some indels!
Comment
-
Any luck with soap on indels?
I tried it on my paired-end data, but soapsnp ends up in segmentation fault!
I think I did fine on the sort (confused about sorting a paired end alignment on coordinates!) .. does soap not use the information of pairs after mapping them!--
bioinfosmComment
-
Hi, more SOAP,
The SOAP2 paper states that the new SOAP2 supports several input and output formats:
The output formats include a SOAP tab-delimited
text table, a gzipped text table, a Sequence Alignment/Map (SAM)
format and its binary equivalent (BAM) that is recommended by
the 1000 Genomes Consortium, and a Consed format that fits with
the assembly viewer.
Does anybody know how to select those formats? I have not been able to find any info on the documentation or web site.
Thanks!!Comment
-
By the way this is the link to SOAP2 version 2.19
Cheers!Comment
-
Does SOAP2 perform gapped alignments yet?Comment
-
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM
Comment