rename option. support (b)gzipped input

Author: brentp

README.md

@@ -2,6 +2,36 @@
 
 [![badge](https://img.shields.io/badge/docs-latest-blue.svg)](https://brentp.github.io/libbigwig-nim/bigwig.html)
 
+## Command Line
+
+bigwig-nim includes a command-line tool distributed as a static binary. It supports converting
+bed to bigwig and bigwig to bed and extracting stats (mean, coverage, etc) for regions in a bigwig.
+
+There are other tools to do this, including [kentTools](https://hgwdev.gi.ucsc.edu/~kent/src/) which has a more restrictive license and does not supported (b)gzipped input and [bwtools](https://github.com/CRG-Barcelona/bwtool) which seems to provide similar functionality (but I am not able to build it).
+
+
+### view 
+
+To convert a bed with the value in the 4th column to bigwig, use:
+
+```Shell
+bigwig view $bed_in --value-column 4 --chrom-sizes $fai -O bigwig -o $bigwig_out
+```
+`bigwig` will automatically determine the best data format for each block (fixed span and step or per-base) most of the
+CPU time is spent parsing the input bed file.
+
+### stats
+
+To get the mean value for a given region (in this case on chromosome 22)
+
+```Shell
+bigwig stats --stat mean $bigwig 22:145000-155000
+```
+
+The supported stats are `mean`, `min`, `max`, `coverage`, `sum` with a special-case for the stat of `header` which
+shows the chromosomes, lengths and mean coverages for each chromosome in the bigwig file.
+
+
 ## Reading
 
 ```Nim

bigwig.nimble

@@ -18,7 +18,7 @@ license       = "MIT"
 
 # Dependencies
 
-requires "nimbigwig", "argparse"
+requires "nimbigwig", "argparse", "hts >= 0.2.20"
 srcDir = "src"
 installExt = @["nim"]
 

src/bigwigpkg/cli.nim

@@ -2,6 +2,7 @@ import strutils
 import tables
 import strformat
 import ./lib
+import hts/files
 import argparse
 
 type region = tuple[chrom: string, start: int, stop: int]
@@ -54,8 +55,7 @@ iterator chunks(bed_path: string, chrom: var string, n:int=2048, value_column: i
   let col = value_column - 1
 
   var cache = newSeqOfCap[tuple[start: int, stop:int, value:float32]](n)
-  # TODO: support gzipped as well.
-  for l in bed_path.lines:
+  for l in bed_path.hts_lines:
     let toks = l.strip.split('\t')
     if toks[0] != chrom and cache.len > 0:
       yield cache
@@ -215,7 +215,7 @@ proc view_main*() =
 
   var p = newParser("bigwig view"):
     option("-r", "--region", help="optional chromosome, or chrom:start-stop region to view")
-    option("-f", "--fai", help="path to fai, only used for converting BED->BigWig")
+    option("-c", "--chrom-sizes", help="file indicating chromosome sizes (can be .fai), only used for converting BED->BigWig")
     option("-i", "--value-column", help="column-number (1-based) of the value to encode in to BigWig, only used for encoding BED->BigWig", default="4")
     option("-O", "--output-fmt", choices= @["bed", "bigwig"], default="bed", help="output format")
     option("-o", "--output-file", default="/dev/stdout", help="output bed or bigwig file")
@@ -283,11 +283,11 @@ proc view_main*() =
       ofh.close
     bw.close
   else:
-    if opts.fai == "":
-      quit "[bigwig] --fai is required when input is not bigwig."
+    if opts.chrom_sizes == "":
+      quit "[bigwig] --chrom-sizes is required when input is not bigwig."
     if opts.region != "":
       quit "[bigwig] --region is not supported for BED input"
-    var h = opts.fai.from_fai
+    var h = opts.chrom_sizes.from_fai
     var ofh: BigWig
     if  not ofh.open(opts.output_file, fmWrite):
       quit "[bigwig] couldn't open output bigwig file:" & opts.output_file