BamCramConvert: easy bam2cram conversion

v1.3.1

Update README.md

BamCramConvert: easy bam2cram conversion

• improved logging system and added verbosity options
• code cleaning
• added some additional checkings (and possibility to disable fasta ref checking using -drc)

v1.2

• Adds crumble capacities to bcc (invoke using -uc and optionally provide path to crumble using -cp)

v1.1

This release adds 2 major functionalities:

• genome versions of the file to be converted and of the reference used by bcc.sh (provided with the -fa option) are checked before conversion, based on chr1 length (works for hg19 and hg38 only)
• added the possibility to check conversion using a modified version of bam2cram-check

v1.0

converts bam2cram and cram2bam using samtools:

• performs bam/cram researches in several directories using UNIX find, managing size and last modification date (-s, -mt)
• can generate srun commands (-sl)
• can handle samtools -@ option (-th)
• can suppress (rm) original file - beware, only based on samtools command successexit status