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chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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--methy_extract writes files to the wrong place #16

Open antonkulaga opened 5 years ago

antonkulaga commented 5 years ago

--methy_extract writes output inside bmm folder I give to it instead of writing to current working folder. For instance if I have:


/opt/BitMapperBS/bitmapperBS --methy_extract /data/indexes/homo_sapiens --bmm_folder /data/bmms --seq   --seq1 /data/samples/SRR948855/SRR948855_1.fastq_cleaned.fastq.gz --seq2 /data/samples/SRR948855/SRR948855_2.fastq_cleaned.fastq.gz --sensitive --pe
``` while current working folder is "my_methylation_analysis_1" it will write output_CpG.bedGraph   not into "my_methylation_analysis/" but to /data/bmms folder.
chhylp123 commented 5 years ago

--methy_extract writes output inside bmm folder I give to it instead of writing to current working folder. For instance if I have:

/opt/BitMapperBS/bitmapperBS --methy_extract /data/indexes/homo_sapiens --bmm_folder /data/bmms --seq   --seq1 /data/samples/SRR948855/SRR948855_1.fastq_cleaned.fastq.gz --seq2 /data/samples/SRR948855/SRR948855_2.fastq_cleaned.fastq.gz --sensitive --pe
``` while current working folder is "my_methylation_analysis_1" it will write output_CpG.bedGraph   not into "my_methylation_analysis/" but to /data/bmms folder.

This problem has been solved. Please try version 1.0.2.2 : )