Glimpse/htslib retries & bug fix, and index specification

[kachulis]

A few changes here.

• implements use of ##idx## to specify cram index
• updates glimpse docker for retries and to fix bug which can lead to partial reading of crams from cloud storage (see odelaneau/GLIMPSE#212)
• adds coverage metrics as additional output to try to catch any potential issues like this in future
• check for "EOF marker missing" message from htslib which occurs with one remaining edge case read failure which cannot otherwise be caught
• some updates to docker building to be able to build on m1 mac (for linux/amd64)

might worth adding a check on the coverage metrics to Glimpse2CheckQC. I can do that in a separate pr.