d4: write sfi index

• write sfi index in d4 files (#243 thanks @cademirch)

fix for d4

v0.3.9

• fix d4 output (#237)
• (thanks for @kojix2 for fixes on docopt and for nim >=2)

fix for bams/crams with *many* contigs

v0.3.8

• mosdepth is now much faster on bams/crams with a large number of contigs (#229)

thanks @ohickl for reporting and providing a test-case.

support cram v 3.1

v0.3.7

• support CRAM v3.1. only updates htslib that binary is built with to v1.19.1 (#224 thanks @adthrasher for reporting and testing)

filter on fragment length

v0.3.6

• allow filtering on fragment length thanks @LudvigOlsen for implementing! (#214)
• fix bug where empty chromosomes are not reported as having 0 depth (#216)

The new optional arguments:

  -l --min-frag-len <min-frag-len>  minimum insert size. reads with a smaller insert size than this are ignored [default: -1]
  -u --max-frag-len <max-frag-len>  maximum insert size. reads with a larger insert size than this are ignored. [default: -1]

summary min_depth on regions

v0.3.5

• fix bug with summary min for regions (#207 thanks to Xavier for supplying test-case)

v0.3.4

v0.3.4

• bump version for build supporting gs:// urls
• dont error on regions larger than chromosome.

custom index location

v0.3.3

• allow specifying a custom index by passing '/path/to/bam##idx##/other-path/to/index.bai'

readgroups fix

when using read-groups, there was an intermittent error that would sometimes skip reads.
thanks @chrisamiller for reporting and providing a test-case.

bugfix

• fix bug with regions and d4 that would cause error even when --d4 was not used.