Merge pull request #264 from brentp/pr261

set TBX_UCSC preset for bed

Author: brentp

functional-tests.sh

@@ -12,8 +12,8 @@ set -o nounset
 
 
 set -e
-nim c --boundChecks:on -x:on -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo --mm:refc mosdepth.nim
-nim c -x:on --mm:refc -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/funcs.nim
+nim c -a --boundChecks:on -x:on -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo --mm:refc mosdepth.nim
+nim c -a -x:on --mm:refc -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/funcs.nim
 set +e
 exe=./mosdepth
 bam=/data/human/NA12878.subset.bam

mosdepth.nim

@@ -18,6 +18,13 @@ when defined(d4):
 var precision: int
 var output_summary_header = true
 
+const
+  TbxUcscPreset* = 0x10000'i32
+
+proc set_bed_tbx_preset*(bgzi: var BGZI) {.inline.} =
+  if bgzi != nil:
+    bgzi.csi.tbx.conf.preset = TbxUcscPreset
+
 try:
   var tmp = getEnv("MOSDEPTH_PRECISION")
   precision = parse_int(tmp)
@@ -636,14 +643,17 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, min_len: int, max_len: int,
     else:
       fbase = wopen_bgzi(prefix & ".per-base.bed.gz", 1, 2, 3, true,
           compression_level = 1, levels = levels)
+      fbase.set_bed_tbx_preset()
     #open(fbase, prefix & ".per-base.bed.gz", "w1")
   if quantize.len != 0:
     fquantize = wopen_bgzi(prefix & ".quantized.bed.gz", 1, 2, 3, true,
         compression_level = 1, levels = levels)
+    fquantize.set_bed_tbx_preset()
 
   if thresholds.len != 0:
     fthresholds = wopen_bgzi(prefix & ".thresholds.bed.gz", 1, 2, 3, true,
         compression_level = 1, levels = levels)
+    fthresholds.set_bed_tbx_preset()
     fthresholds.write_header(thresholds)
 
   if not open(fh_global_dist, prefix & ".mosdepth.global.dist.txt", fmWrite):
@@ -659,6 +669,7 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, min_len: int, max_len: int,
   if region != "":
     fregion = wopen_bgzi(prefix & ".regions.bed.gz", 1, 2, 3, true,
         levels = levels)
+    fregion.set_bed_tbx_preset()
     if region.isdigit():
       window = uint32(S.parse_int(region))
     else:
@@ -969,4 +980,3 @@ 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)
-

nim.cfg

@@ -1,6 +1,13 @@
 # in htslib: ./configure --with-libdeflate --disable-libcurl
 # nim c -a -d:static -d:release mosdepth.nim
 mm:refc
+#nimcache:"nimcache"
+
+@if gcc:
+  # GCC 14 rejects some older docopt-generated C pointer conversions.
+  passC:"-Wno-incompatible-pointer-types"
+@end
+
 @if static:
   passC:"-static"
   passl:"-static"

tests/funcs.nim

@@ -2,6 +2,7 @@ import unittest
 import mosdepth
 import depthstat
 import os
+import hts
 
 suite "mosdepth-suite":
 
@@ -89,3 +90,19 @@ suite "mosdepth-suite":
     check r.chrom == "Super-Scaffold_52"
     check r.start == 1
     check r.stop == 1000
+
+  test "bed-index-preset":
+    let path = getTempDir() / "mosdepth-index-preset.bed.gz"
+    if fileExists(path):
+      removeFile(path)
+    if fileExists(path & ".csi"):
+      removeFile(path & ".csi")
+    var fh = wopen_bgzi(path, 1, 2, 3, true)
+    fh.set_bed_tbx_preset()
+    check fh.write_interval("chr1\t0\t1\t0.0", "chr1", 0, 1) >= 0
+    check fh.csi.tbx.conf.preset == TbxUcscPreset
+    discard fh.close()
+    if fileExists(path):
+      removeFile(path)
+    if fileExists(path & ".csi"):
+      removeFile(path & ".csi")