From 33b2db1c6042ef40aace870b3dc62bf7f97a66ec Mon Sep 17 00:00:00 2001
From: Clyybber <darkmine956@gmail.com>
Date: Wed, 2 Oct 2019 00:02:03 +0200
Subject: [PATCH] Prepare for csize to be uint

See https://github.com/nim-lang/Nim/pull/12321
---
 src/hts/bam.nim       | 2 +-
 src/hts/bgzf/bgzi.nim | 2 +-
 src/hts/vcf.nim       | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/hts/bam.nim b/src/hts/bam.nim
index f609273..6136854 100644
--- a/src/hts/bam.nim
+++ b/src/hts/bam.nim
@@ -67,7 +67,7 @@ proc from_string*(r:Record, record_string:string) =
       raise newException(ValueError, "must create record with NewRecord before calling from_string")
 
 
-    var kstr = kstring_t(s:record_string.cstring, m:record_string.len, l:record_string.len)
+    var kstr = kstring_t(s:record_string.cstring, m:record_string.len.csize, l:record_string.len.csize)
     var ret = sam_parse1(kstr.addr, r.hdr.hdr, r.b)
     if ret != 0:
       raise newException(ValueError, "error:" & $ret & " in from_string parsing record: " & record_string)
diff --git a/src/hts/bgzf/bgzi.nim b/src/hts/bgzf/bgzi.nim
index a33979c..b3320fe 100644
--- a/src/hts/bgzf/bgzi.nim
+++ b/src/hts/bgzf/bgzi.nim
@@ -51,7 +51,7 @@ iterator query*(bi: BGZI, chrom: string, start:int, stop:int): string {.inline.}
     fastSubStr(outstr, kstr.s, 0, int(kstr.l))
     yield outstr
   hts_itr_destroy(itr)
-  assert kstr.l >= 0
+  assert int(kstr.l) >= 0
   free(kstr.s)
   assert fn.addr != nil
 
diff --git a/src/hts/vcf.nim b/src/hts/vcf.nim
index 8a3d873..b44c35f 100644
--- a/src/hts/vcf.nim
+++ b/src/hts/vcf.nim
@@ -199,7 +199,7 @@ proc toSeq[T](data: var seq[T], p:pointer, n:int) {.inline.} =
   if data.len != n:
     data.set_len(n)
   if n == 0: return
-  copyMem(data[0].addr, p, (n * sizeof(T).csize))
+  copyMem(data[0].addr, p, csize(n * sizeof(T)))
 
 proc bcf_hdr_id2type(hdr:ptr bcf_hdr_t, htype:int, int_id:int): int {.inline.}=
   # translation of htslib macro.
@@ -403,7 +403,7 @@ proc destroy_variant(v:Variant) =
     free(v.p)
 
 proc from_string*(v: var Variant, h: Header, s:var string) =
-  var str = kstring_t(s:s.cstring, l:s.len, m:s.len)
+  var str = kstring_t(s:s.cstring, l:s.len.csize, m:s.len.csize)
   if v == nil:
     new(v, destroy_variant)
   if v.c == nil: