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  • caswater
    replied
    hi hi, please kindly let me know if you could try it out--- I almost forget everything about C language -_-

    Leave a comment:


  • hanifk
    replied
    Originally posted by tutenkhamun View Post
    I think you will need to open up samtools.h in the breakdancer source code and compare it with bam_index.c in samtools source code. You will need to update the corresponding functions in samtools.h from bam_index.c. In the main BreakdancerMax.cpp, you will need to make sure that the functions ReadBamChr_prep and ReadBamChr work correctly with the new version of samtools. Good luck!
    Oh, I have been confused with this for a long time.
    I will have a try as your suggestion, thank you very much.

    Leave a comment:


  • tutenkhamun
    replied
    I think you will need to open up samtools.h in the breakdancer source code and compare it with bam_index.c in samtools source code. You will need to update the corresponding functions in samtools.h from bam_index.c. In the main BreakdancerMax.cpp, you will need to make sure that the functions ReadBamChr_prep and ReadBamChr work correctly with the new version of samtools. Good luck!

    Leave a comment:


  • caswater
    replied
    thank you. I haven't fixed the problem yet, but just looked at the output from Pindel now.

    Leave a comment:


  • tutenkhamun
    replied
    The problem is because breakdancer has code from an older version of samtools. The BAM index is used for the -o option. Unfortunately, the BAM index format has changed since the last time code was copied from samtools source code into breakdancer source code. I feel this is why breakdancer crashes when run with the -o option. I don't know which version of samtools the index reading code in breakdancer corresponds to, though.

    Leave a comment:


  • hanifk
    replied
    I have the same problem with you, did you have fixed it?

    Leave a comment:


  • caswater
    started a topic breakdancer - empty output?

    breakdancer - empty output?

    Hi, I just ran breakDancer on a bam file. The program ran for a while, but gave out nothing in its input.

    The configure file (manually configured as described on its website) is:

    map:my.bam mean:334 std:44 readlen:
    100.00 sample:mySample exe:samtools view

    I then used the following commands to call inter-chromosomal translocation:

    breakdancer_max -t -q 20 -r 10 config > result.txt

    However, after several hours, the program quit without notifying anything, and the result.txt is just like:
    #Software: BreakDancerMax-1.1r112
    #Command: breakdancer_max -t -q 20 -r 10 config
    #Library Statistics:
    #Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib recal.bam

    It didn't give any output except for the headers. Do you have any experience with it? Thank you very much

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