Error in naming of processed BAM samples

[ChaochihL]

Type of issue

• [x] Bug
• [ ] Feature request

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Bugs

Have you looked at the wiki?

The wiki is located here

• [ ] Yes
• [ ] No

  Which handler are you having trouble with?

Process_SAM

Describe your problem

What is the error message being generated?

-bash-4.1$ ./sequence_handling 7 ~/Config_125bp 
sequence_handling: Mapping coverage...
/home/morrellp/liux1299/Shared/WBDC_inversions/SAM_Processing/Barley_Inversions_deduped_BAM.txt doesn't exist, exiting...

Copy the part of the config file used by this handler

28 #   Where is the list of processed BAM samples?
     29 #       This is used for Coverage_Map and Indel_Realignment
     30 #       If using SAM_Processing, then leave as is
     31 BAM_SAMPLES=${OUT_DIR}/SAM_Processing/${PROJECT}_deduped_BAM.txt

Currently the output name is called:

Barley_Inversions_Processed_BAM.txt

#   Handler-specific values go here

#   Dependency definitions go here

Has anyone else been able to replicate your error?

• [ ] Yes
• [ ] No

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Feature requests

What new thing is being added?

• [ ] New handler
• [ ] Modification to handler

  Describe the changes made

  Where does this fit in with the existing pipeline?

  List any dependencies that will be needed for this change, providing links to the source code as needed

  Do you have a script for this change? Please note that we can implement your code faster if you write everything as BASH functions.

• [ ] Yes
• [ ] No

If yes, please make sure the code is posted online and link to it below:

name of code exerpt

Good hosting sites are GitHub and GitHub Gist.

Thank you for your help improving sequence_handling!

[mojaveazure]

Fixed.