Re: [Seqan-dev] problem to use BamRecordToAlignment

[marion dubarry <dubarry.ma@gmail.com>]

BamFileIn bamFileIn;
    if (!open(bamFileIn,File.c_str())){
        cout << "Error : Cannot open " << File << endl;
        exit(1);
    }

I don't think this is the error because I can read the headers, or the records. Just the bamRecordToAlignment() function fail

2015-04-21 12:57 GMT+02:00 Jordan Willis <jwillis0720@gmail.com>:

Hi,

Where is you bamFileIn defined?

On Apr 21, 2015, at 3:46 AM, marion dubarry <dubarry.ma@gmail.com> wrote:

Hello,

I think I have a basic question, sorry in advance. I don't understand what is suppose to contain "references" of a record from the methods BamRecordToAlignment().

Reference is suppose to contain : "The string with the reference that record lies on."

I start with the example and I modify it :

  BamAlignmentRecord record;
  StringSet<Dna5String> references;
  Align<Dna5String> align;
  while (!atEnd(bamFileIn))
  {
        readRecord(record, bamFileIn);
        appendValue(references,record.seq);

       if (record.rID != BamAlignmentRecord::INVALID_REFID)
               bamRecordToAlignment(align, references[record.rID], record);
    }

I try a lot of think for the variable "references", this is my last try. Because references is of type Dna5String. I try a lot of things (most of time absurd things) and I obtain always this error :
seqan-src/include/seqan/sequence/string_base.h:429 Assertion failed : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) was: 1 >= 1 (Trying to access an element behind the last one!)
Aborted (core dumped)

I think the problem come from my variable references, could you explain me what is it suppose to contain ?

Thanks,

Sorry for my (stupid) question,

Marion

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