AUGUSTUS Forum

Posted: **Fri Nov 20, 2015 1:20 pm**

Originally posted in the old forum by Fred on 21.12.2012 - 22:18
when trying to run bamtools filter -in output_directory/accepted_hits.bam -out output_directory/accepted_hits.noN.bam -script operation_N_filter.txt
I receive the following error:
bamtools filter ERROR: could not open script: operation_N_filter.txt for reading

Code: Select all

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct NULL not valid

Aborted (core dumped)

Posted: **Fri Nov 20, 2015 1:20 pm**

by Fred on 21.12.2012 - 22:51
bamtools filter
Is the operation_N_filter.txt script in the bamtools toolkit or is this an external script.

Posted: **Fri Nov 20, 2015 1:20 pm**

by katharina on 28.12.2012 - 17:55
This is an external script, but it has very simple contents:

Code: Select all

{ 
"filters" :
	[
	  { "id" 		: 	"operation_N",
		"cigar" 	: 	"*N*"
	  },

	  { "id" 		: 	"is_Mapped",
		"isMapped" 	:	"true"
	  }

	],
"rule" :	"!operation_N & is_Mapped" 
}

Posted: **Fri Nov 20, 2015 1:21 pm**

by Fred on 31.12.2012 - 00:07
Great. This is what I was looking for. Thanks!

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