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afujimoto / CAMPHORsomatic

GNU General Public License v3.0
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CAMPHOR has hardcoded paths to samtools and other resources in source #2

Open oneillkza opened 3 years ago

oneillkza commented 3 years ago

In src:

$ grep fujimoto *
compare_with_normal.INS.py: cmd = "/share/amed_snt/WORK/fujimoto/src/tools/samtools-0.1.6/samtools view " + bam + " " + chr + ":" + pos + "-" + pos
compare_with_normal.old.py:#    cmd = "/share/amed_snt/WORK/fujimoto/src/tools/samtools-0.1.6/samtools view " + bam + " " + chr + ":" + pos + "-" + pos
compare_with_normal.py:#    cmd = "/share/amed_snt/WORK/fujimoto/src/tools/samtools-0.1.6/samtools view " + bam + " " + chr + ":" + pos + "-" + pos
INV_filter3.py:#        print("samtools view /share/amed_snt/WORK/fujimoto/nanopore/180615/RK014_C_WGS.All/RK014_C_WGS.All.fastq.minimap2.merge.sort.bam ", line_l[0] + ":" + str(int(line_l[1]) - 1000) + "-" + str(int(line_l[1]) + 1000), " > /share/amed_snt/WORK/fujimoto/nanopore/180908/RK014_C_" + line_l[0] + "_" + line_l[1] + ".sam")    
INV_filter3.py:#        print("samtools view /share/amed_snt/WORK/fujimoto/nanopore/180615/RK014_C_WGS.All/RK014_C_WGS.All.fastq.minimap2.merge.sort.bam ", line_l[2] + ":" + str(int(line_l[3]) - 1000) + "-" + str(int(line_l[3]) + 1000), " > /share/amed_snt/WORK/fujimoto/nanopore/180908/RK014_C_" + line_l[2] + "_" + line_l[3] + ".sam")

This causes errors, such that the example data produces an empty somatic_SV.vcf

afujimoto commented 3 years ago

Thank you for this comment. We fixed the bug.