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ERROR_COUNT segfaults (reusing existing BAM file) #44

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?

breseq ERROR_COUNT -b ref.bam -f ref.fasta --output . --covariates 
ref_base,obs_base --errors --readfile s1.fastq 

What is the expected output? What do you see instead?

Above command segfaults in write_base_qual_only_prob_table() because 
m_covariate_max[k_read_set] is not set correctly (looks like MAX_INT) and 
therefore this_file_name.replace() will fail.

What version of the product are you using? On what operating system?

Breseq 0.16 and 0.18.
CentOS release 6.1

Please provide any additional information below.

I was trying to predict SNVs and low frequency polymorphisms from an already 
existing BAM file and presume that ERROR_COUNT is the first step in the 
pipeline to use.

Original issue reported on code.google.com by andreas....@gmail.com on 15 Jun 2012 at 7:26

GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
Option (--aligned-sam) added as experimental to v0.18b (not provided on 
download page).

Original comment by jeffrey....@gmail.com on 18 Jun 2012 at 9:06