Errors in BAM iterator should be fatal (#265)

* Use personal hts-nim fork

* Exit nonzero if iterator fails due to IO issues

* Bump hts-nim dependency version

* IOError -> BamError

* Revert "Use personal hts-nim fork"

Now that hts-nim PR is merged, we revert the commit that uses my personal fork
(f337ba1), and update to the latest Nimble
version.

* Add comment clarifying try/except block

Author: julianhess

mosdepth.nim

@@ -181,8 +181,14 @@ iterator regions(bam: hts.Bam, region: region_t, tid: int, targets: seq[
     if tid != -1:
       if stop == 0:
         stop = targets[tid].length
-      for r in bam.query(tid, int(region.start), int(stop)):
-        yield r
+      try:
+        for r in bam.query(tid, int(region.start), int(stop)):
+          yield r
+      # if the iterator fails due to an invalid read from the BAM (due to file
+      # corruption or filesystem issues), we want to gracefully exit with a
+      # nonzero return.
+      except hts.BamError:
+        quit getCurrentExceptionMsg()
     else:
       stderr.write_line("[mosdepth]", region.chrom, " not found")
 

mosdepth.nimble

@@ -7,7 +7,7 @@ license       = "MIT"
 
 # Dependencies
 
-requires "hts >= 0.3.29", "docopt == 0.7.1", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.5"
+requires "hts >= 0.3.31", "docopt == 0.7.1", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.5"
 
 bin = @["mosdepth"]
 skipDirs = @["tests"]