search

hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
29 stars 5 forks source link

add summary option #44

Closed fei0810 closed 4 years ago

fei0810 commented 4 years ago

Hi ,

I have tested MapCaller, it is cool. Could you add a summary option such as --summary-file so that user can read alignment summary in a file. I want to use MapCaller in my own pipeline, so i can check the summary file anytime. I try use > mapcaller.log 2>&1, but the log file would save something like below

^M0 paired-end reads have been processed in 0 seconds...

What user really need are: 

All the 3065444296 paired-end reads have been processed in 44220 seconds.
  2796573021 ( 91.22%) reads are mapped properly.
  2496133858 ( 81.42%) reads are mapped in pairs.
        Estimated AvgCoverage = 88
        Duplication rate=69.41%
        Estimated fragment size = 333, insert size = 33
Identify all variants (min_alt_allele_depth=5)...
        Write all the predicted sample variations to file [4sample_mapcaller_raw.vcf]...
        34635289(snp); 1497902(ins); 1344402(del); 6008(trans); 269(inversion)
variant calling has been done in 264 seconds.
All done! It took 44751 seconds to complete the data analysis.

Thankyou!

hsinnan75 commented 4 years ago

Hello, I've updated MapCaller with logging the summary report. Please update your MapCaller. The argument is "-log job.log", default filename is "job.log". Thank you!

fei0810 commented 4 years ago

@hsinnan75 Thank you ! I will try it tomorrow.

fei0810 commented 4 years ago

Hello, I've updated MapCaller with logging the summary report. Please update your MapCaller. The argument is "-log job.log", default filename is "job.log". Thank you!

Hi, the log file is work well now.