CHANGELOG

+changes in version 1.6.1 (2020-01-08)
+
+- Further extension of the C API.
+
+
 changes in version 1.6.0 (2020-01-06)
 
 - improve error handling in some tools

VERSION

-1.6.0
+1.6.1

debian/changelog

+genometools (1.6.1+ds-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Wed, 08 Jan 2020 21:20:57 +0100
+
 genometools (1.6.0+ds-1) unstable; urgency=medium
 
   * New upstream release.

gtdata/modules/gtdoclib/docbase.lua

@@ -22,6 +22,19 @@ local w = require 'warning'
 
 DocBase = {}
 
+function dump(o)
+   if type(o) == 'table' then
+      local s = '{ '
+      for k,v in pairs(o) do
+         if type(k) ~= 'number' then k = '"'..k..'"' end
+         s = s .. '['..k..'] = ' .. dump(v) .. ','
+      end
+      return s .. '} '
+   else
+      return tostring(o)
+   end
+end
+
 function DocBase:new()
   o = {}
   o.classes = {}
@@ -156,7 +169,8 @@ function DocBase:process_ast(ast, be_verbose)
     else
       local keyword = ast[1]
       if be_verbose then
-        print("keyword: " .. keyword)
+        print("keyword: ")
+        print(dump(keyword))
       end
       if keyword == "class" then
         o.last_module = nil

scripts/code_templates.rb

@@ -275,7 +275,7 @@ $interface_file = <<-INTERFACE_CODE
 #include "<%=subdir%>/<%=fkt_pref%>_rep.h"
 
 #include "core/assert_api.h"
-#include "core/class_alloc.h"
+#include "core/class_alloc_api.h"
 #include "core/ma_api.h"
 #include "core/unused_api.h"
 

scripts/gen-intsets.rb

@@ -61,7 +61,7 @@ IMPL = <<-IMPL
 #include "core/ensure_api.h"
 #include "core/intbits.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/unused_api.h"
 #include "extended/intset_<%=bits%>.h"
 #include "extended/io_function_pointers.h"

scripts/mk_ft_longest_common.rb

@@ -25,7 +25,7 @@ def gen_compare(a_mode,b_mode,wildcard,complement)
              " " * 10 + "break"
   if wildcard
     return "const GtUchar cu = #{gen_access_raw(a_mode,"useq","u")};\n" +
-           " " * 8 + "if (cu == WILDCARD ||" + splitter + "cu !=" + splitter +
+           " " * 8 + "if (cu == GT_WILDCARD ||" + splitter + "cu !=" + splitter +
            cmp_expr
   else
     return "if (#{gen_access_raw(a_mode,"useq","u")} !=" + splitter +

scripts/mksainseq.rb

@@ -27,13 +27,13 @@ def getc_call(key,posexpr,seqaccess = false)
     return "(GtUword) array[#{posexpr}]"
   elsif key == "BARE_ENCSEQ"
     if seqaccess
-      return "(GtUword)\nISSPECIAL(tmpcc =\nplainseq[#{posexpr}])\n" +
+      return "(GtUword)\nGT_ISSPECIAL(tmpcc =\nplainseq[#{posexpr}])\n" +
              "  ? GT_UNIQUEINT(#{posexpr}) : (GtUword) tmpcc"
     else
       return "(GtUword)\nplainseq[#{posexpr}]"
     end
   elsif seqaccess
-    return "ISSPECIAL(tmpcc =\ngt_encseq_reader_next_encoded_char(esr))\n" +
+    return "GT_ISSPECIAL(tmpcc =\ngt_encseq_reader_next_encoded_char(esr))\n" +
                " ? GT_UNIQUEINT(#{posexpr}) : (GtUword) tmpcc"
   else
     return "(GtUword) gt_encseq_get_encoded_char(\n" +
@@ -45,7 +45,7 @@ end
 
 def special2unique(key,cc,start)
   if key == "ENCSEQ" || key == "BARE_ENCSEQ"
-    return "if (ISSPECIAL(#{cc})) { #{cc} = GT_UNIQUEINT(#{start}); }"
+    return "if (GT_ISSPECIAL(#{cc})) { #{cc} = GT_UNIQUEINT(#{start}); }"
   else
     return ""
   end

src/annotationsketch/block.c

@@ -25,7 +25,7 @@
 #include "core/ensure_api.h"
 #include "core/log.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/undef_api.h"
 #include "core/unused_api.h"
 

src/annotationsketch/canvas.c

@@ -18,10 +18,10 @@
 #include <math.h>
 #include <string.h>
 #include "core/assert_api.h"
-#include "core/class_alloc.h"
+#include "core/class_alloc_api.h"
 #include "core/ensure_api.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/minmax_api.h"
 #include "core/range_api.h"
 #include "core/str_api.h"

src/annotationsketch/canvas_cairo.c

@@ -21,7 +21,7 @@
 #include "core/ensure_api.h"
 #include "core/log.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/minmax_api.h"
 #include "core/range_api.h"
 #include "core/unused_api.h"

src/annotationsketch/custom_track.c

@@ -18,7 +18,7 @@
 #include "annotationsketch/custom_track_rep.h"
 #include "annotationsketch/custom_track.h"
 #include "core/assert_api.h"
-#include "core/class_alloc.h"
+#include "core/class_alloc_api.h"
 #include "core/ma_api.h"
 #include "core/unused_api.h"
 

src/annotationsketch/custom_track_gc_content.c

@@ -23,7 +23,7 @@
 #include "core/class_alloc_lock.h"
 #include "core/log.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/minmax_api.h"
 #include "core/unused_api.h"
 
@@ -57,7 +57,7 @@ static double get_val_for_pos(GtCustomTrackGcContent *ctgc, GtUword pos)
     }
     bases++;
   }
-  return ((double) gc_count)/((double) MIN(ctgc->windowsize, bases));
+  return ((double) gc_count)/((double) GT_MIN(ctgc->windowsize, bases));
 }
 
 int gt_custom_track_gc_content_sketch(GtCustomTrack *ct, GtGraphics *graphics,

src/annotationsketch/drawing_range.c

@@ -16,7 +16,7 @@
 */
 
 #include "core/assert_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "annotationsketch/drawing_range.h"
 
 int gt_drawing_range_compare(GtDrawingRange range_a, GtDrawingRange range_b)

src/annotationsketch/element.h

@@ -26,7 +26,7 @@ typedef struct GtElement GtElement;
 #include "annotationsketch/drawing_range.h"
 #include "core/range_api.h"
 #include "core/strand_api.h"
-#include "extended/feature_type.h"
+#include "extended/feature_type_api.h"
 #include "extended/genome_node.h"
 
 /* Creates a complete new <GtElement> object. */

src/annotationsketch/graphics.c

@@ -16,7 +16,7 @@
 */
 
 #include "core/assert_api.h"
-#include "core/class_alloc.h"
+#include "core/class_alloc_api.h"
 #include "core/ma_api.h"
 #include "core/thread_api.h"
 #include "core/unused_api.h"

src/annotationsketch/graphics_cairo.c

@@ -35,7 +35,7 @@
 #include "core/file_api.h"
 #include "core/fileutils_api.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/minmax_api.h"
 #include "core/str_api.h"
 #include "core/unused_api.h"

src/annotationsketch/gt_sketch.c

@@ -28,7 +28,7 @@
 #include "core/splitter.h"
 #include "core/undef_api.h"
 #include "core/unused_api.h"
-#include "core/versionfunc.h"
+#include "core/versionfunc_api.h"
 #include "core/warning_api.h"
 #include "extended/add_introns_stream_api.h"
 #include "extended/bed_in_stream.h"

src/annotationsketch/gt_sketch_page.c

@@ -27,18 +27,18 @@
 #if CAIRO_HAS_SVG_SURFACE
 #include <cairo-svg.h>
 #endif
-#include "core/bioseq.h"
+#include "core/bioseq_api.h"
 #include "core/cstr_api.h"
 #include "core/fileutils_api.h"
 #include "core/gtdatapath.h"
 #include "core/log.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/option_api.h"
 #include "core/str_api.h"
 #include "core/unused_api.h"
 #include "core/undef_api.h"
-#include "core/versionfunc.h"
+#include "core/versionfunc_api.h"
 #include "core/warning_api.h"
 #include "annotationsketch/canvas_cairo_context.h"
 #include "annotationsketch/custom_track_gc_content_api.h"

src/annotationsketch/image_info.c

@@ -19,11 +19,11 @@
 #include "core/array.h"
 #include "core/ensure_api.h"
 #include "core/ma_api.h"
-#include "core/mathsupport.h"
+#include "core/mathsupport_api.h"
 #include "core/range_api.h"
 #include "core/strand_api.h"
 #include "core/unused_api.h"
-#include "extended/feature_type.h"
+#include "extended/feature_type_api.h"
 #include "extended/genome_node.h"
 
 struct GtImageInfo {