Shifu Chen

This isn't a common requirement, so it won't be implemented immediately. Probably you can visualize the results using Python or other programming scripts to parse the JSON outputs.

The version you have is the latest v0.4.0. I will add an option `--version` to display the version.

@ZKai0801 Can you please check and fix this issue?

> Just found out that I did not fully fix the strand issue, should have added strand to the identification of the longest transcript as well: > > ``` >...

Merged.

I just tried again with command: `./genefuse -r ~/data/ref/hg19.fa -1 ~/data/fq/genefuse.R1.fq.gz -2 ~/data/fq/genefuse.R2.fq.gz -h test.html -j test.json -f genes/druggable.hg19.csv` and got: ``` 15:1:4 start with 4 threads 15:1:47 mapper indexing...

Can you guys check md5 for the downloaded FASTQ file?

http://opengene.org/dataset.html You should download following files: Paired-end FASTQ files for GeneFuse testing (Illumina platform) genefuse.R1.fq.gz (size: 62 M, MD5: 171e6dfa0af37fe95c826005bc5fcdf9) genefuse.R2.fq.gz (size: 66 M, MD5: e756cf01e256186dccaa9e700d85a342)

The druggable.hg19.csv is in the `genes` folder Have you checked the error message?

I mean, you should run: ./genefuse -r Homo_sapiens_assembly19.fasta -f genes/druggable.hg19.csv -1 genefuse.R1.fq.gz -2 genefuse.R2.fq.gz -h report.html >result