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wwylab / MuSE

Somatic point mutation caller
GNU General Public License v2.0
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Fix header: MuSE call generates a MuSe.txt file with incorrect filenames. #19

Closed mdascenzo closed 4 months ago

mdascenzo commented 4 months ago

Current version of MuSE call generates a MuSe.txt file with incorrect filenames. Below is an example, where the filenames recorded for TUMOR and NORMAL are being pulled from first and second input parameters. 

##MuSE_call="MuSE -f /reference_files/GRCh38.d1.vd1/GRCh38.d1.vd1.fa -O pair1 call tumor1_paired.bwa.sorted.dedup.bqsr.bam normal1_paired.bwa.sorted.dedup.bqsr.bam"
##TUMOR="Sample=tumor1,File=-f"
##NORMAL="Sample=normal1,File=/reference_files/GRCh38.d1.vd1/GRCh38.d1.vd1.fa"

After applying the changes in this pull request the header output now shows:

##MuSE_call="MuSE -f /reference_files/GRCh38.d1.vd1/GRCh38.d1.vd1.fa -O pair1 call tumor1_paired.bwa.sorted.dedup.bqsr.bam normal1_paired.bwa.sorted.dedup.bqsr.bam"
##TUMOR="Sample=tumor1,File=tumor1_paired.bwa.sorted.dedup.bqsr.bam"
##NORMAL="Sample=normal1,File=normal1_paired.bwa.sorted.dedup.bqsr.bam"

Please consider this fix which uses an alternate index variable for argv in the WriteHeader function of muse_call.cpp.

jiyunmaths commented 4 months ago

Thank you for fixing this bug.