prep for release

Author: brentp

CHANGES.md

@@ -1,3 +1,7 @@
+v0.3.11
+=======
++ add --fragment-mode (#246 from @LudvigOlsen). calculates coverage over a full fragment, including insert.
+
 v0.3.10
 =======
 + write sfi index in d4 files (#243)

README.md

@@ -23,7 +23,7 @@ when appropriate, the output files are bgzipped and indexed for ease of use.
 ## usage
 
 ```
-mosdepth 0.3.9
+mosdepth 0.3.11
 
   Usage: mosdepth [options] <prefix> <BAM-or-CRAM>
 
@@ -46,13 +46,13 @@ Common Options:
   -n --no-per-base           dont output per-base depth. skipping this output will speed execution
                              substantially. prefer quantized or thresholded values if possible.
   -f --fasta <fasta>         fasta file for use with CRAM files [default: ].
-  --d4                       output per-base depth in d4 format.
 
 Other options:
 
   -F --flag <FLAG>                  exclude reads with any of the bits in FLAG set [default: 1796]
   -i --include-flag <FLAG>          only include reads with any of the bits in FLAG set. default is unset. [default: 0]
   -x --fast-mode                    dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).
+  -a --fragment-mode                count the coverage of the full fragment including the full insert (proper pairs only).
   -q --quantize <segments>          write quantized output see docs for description.
   -Q --mapq <mapq>                  mapping quality threshold. reads with a quality less than this value are ignored [default: 0]
   -l --min-frag-len <min-frag-len>  minimum insert size. reads with a smaller insert size than this are ignored [default: -1]

mosdepth.nim

@@ -844,7 +844,7 @@ when(isMainModule):
   when not defined(release) and not defined(lto):
     stderr.write_line "[mosdepth] WARNING: built in debug mode; will be slow"
 
-  let version = "mosdepth 0.3.10"
+  let version = "mosdepth 0.3.11"
   let env_fasta = getEnv("REF_PATH")
   var doc = format("""
   $version
@@ -965,4 +965,4 @@ Other options:
 
   main(bam, chrom, mapq, min_len, max_len, eflag, iflag, region, thresholds,
       fast_mode, args, use_median = use_median, fragment_mode = fragment_mode, use_d4 = use_d4)
-      
+      

mosdepth.nimble

@@ -1,6 +1,6 @@
 # Package
 
-version       = "0.3.10"
+version       = "0.3.11"
 author        = "Brent Pedersen"
 description   = "fast depth"
 license       = "MIT"