v0.8

The new release ImReP-0.8 includes the following new features:

• imrep-bam.sh (a wrapper to run ImReP for bam file with mapped and unmapped reads) is retired.
• The functionality of imrep-bam.sh is now integrated into imrep.py
• --digGold and -a options have been added allowing to restore the unmapped reads from mapped reads using original raw reads (all reads)

Also, minor bugs remaining from the previous release were fixed.

v0.7

The new release ImReP-0.7 includes the following new features:

• the - f FILTERTHRESHOLD option which allows specifying outlier clonotypes based on their read count
• the --noCast option which allows the user to skip the clustering post-assembly step
• Manual has been updated
• clonality.py has been added allowing to estimate clonality of the sample based on the assembled CDR3 and their relative frequencies

Also, minor bugs remaining from the previous release were fixed.

v0.5.1

This is a maintenance release with the minor changes.

• Bug in imrep-bam.sh was fixed. The path to samtools was incorrect.

v0.5

ImReP 0.5 is available for download here. This is a new release with the following fixes and changes:

• support new format; bam files with a mixture of mapped unmapped reads. Bam with reads mapped to hg19 and hg38 are supported. Use : imrep4bam.sh
• the -r option (imrep4bam.sh) was added to support hg19 or hg39 releases
• Documentation about new format was added here: https://github.com/mandricigor/imrep/wiki/Run-ImReP-for-bams-%28with--mapped-and-unmapped-reads%29

05/20/2017

Bug in imrep-bam.sh was fixed. The path to samtools was incorrect.