Working through issues with GenomeTools feature streams and memory mangement.

streamtest-data.gff3

##gff-version   3
##sequence-region   seq01 1 900
##sequence-region   seq02 1 900
##sequence-region   seq03 1 900
##sequence-region   seq04 1 900
##sequence-region   seq05 1 900
##sequence-region   seq06 1 900
##sequence-region   seq07 1 2000
##sequence-region   seq08 1 2000
##sequence-region   seq09 1 2000
##sequence-region   seq10 1 2000
##sequence-region   seq11 1 2000
##sequence-region   seq12 1 2000
##sequence-region   seq13 1 1500
##sequence-region   seq14 1 1500
##sequence-region   seq15 1 1500
##sequence-region   seq16 1 1500
##sequence-region   seq17 1 1500
##sequence-region   seq18 1 1500
##sequence-region   seq19 1 1500
##sequence-region   seq20 1 1001
##sequence-region   seq21 1 1000
##sequence-region   seq22 1 999
##sequence-region   seq23 1 801
##sequence-region   seq24 1 800
##sequence-region   seq25 1 799
#
seq01	nano	mRNA	400	600	.	+	.	ID=test1.1
seq02	nano	mRNA	401	600	.	+	.	ID=test1.2
seq03	nano	mRNA	402	600	.	+	.	ID=test1.3
seq04	nano	mRNA	200	600	.	+	.	ID=test1.4
seq05	nano	mRNA	201	600	.	+	.	ID=test1.5
seq06	nano	mRNA	202	600	.	+	.	ID=test1.6
#
seq07	nano	mRNA	400	600	.	+	.	ID=test2.1a
seq07	nano	mRNA	1202	1400	.	+	.	ID=test2.1b
seq08	nano	mRNA	400	600	.	+	.	ID=test2.2a
seq08	nano	mRNA	1201	1400	.	+	.	ID=test2.2b
seq09	nano	mRNA	400	600	.	+	.	ID=test2.3a
seq09	nano	mRNA	1200	1400	.	+	.	ID=test2.3b
#
seq10	nano	mRNA	400	600	.	+	.	ID=test3.1a
seq10	nano	mRNA	1002	1300	.	+	.	ID=test3.1b
seq11	nano	mRNA	400	600	.	+	.	ID=test3.2a
seq11	nano	mRNA	1001	1300	.	+	.	ID=test3.2b
seq12	nano	mRNA	400	600	.	+	.	ID=test3.3a
seq12	nano	mRNA	1000	1300	.	+	.	ID=test3.3b
#
seq13	nano	mRNA	400	600	.	+	.	ID=test4.1a
seq13	nano	mRNA	803	1100	.	+	.	ID=test4.1b
seq14	nano	mRNA	400	600	.	+	.	ID=test4.2a
seq14	nano	mRNA	802	1100	.	+	.	ID=test4.2b
seq15	nano	mRNA	400	600	.	+	.	ID=test4.3a
seq15	nano	mRNA	801	1100	.	+	.	ID=test4.3b
seq16	nano	mRNA	400	600	.	+	.	ID=test4.4a
seq16	nano	mRNA	800	1100	.	+	.	ID=test4.4b
#
seq17	nano	mRNA	400	600	.	+	.	ID=test5.1a
seq17	nano	mRNA	606	1000	.	+	.	ID=test5.1b
seq18	nano	mRNA	400	600	.	+	.	ID=test5.2a
seq18	nano	mRNA	602	1000	.	+	.	ID=test5.2b
seq19	nano	mRNA	400	600	.	+	.	ID=test5.3a
seq19	nano	mRNA	601	1000	.	+	.	ID=test5.3b
#
seq20	nano	mRNA	400	600	.	+	.	ID=test6.1
seq21	nano	mRNA	400	600	.	+	.	ID=test6.2
seq22	nano	mRNA	400	600	.	+	.	ID=test6.3
seq23	nano	mRNA	400	600	.	+	.	ID=test6.4
seq24	nano	mRNA	400	600	.	+	.	ID=test6.5
seq25	nano	mRNA	400	600	.	+	.	ID=test6.6
#

streamtest.c

#include "genometools.h"

// gcc -Wall -g -I /usr/local/include/genometools/ -DWITHOUT_CAIRO -o streamtest streamtest.c -lgenometools
// valgrind ./streamtest streamtest-data.gff3 25 > test.txt 2> test.log

int main(int argc, const char **argv)
{
  const char *infile;
  GtError *error;
  GtFeatureIndex *fi1, *fi2, *fi3;
  GtNodeStream *gff3, *s1, *s2, *s3;
  GtStrArray *seqids;
  GtUword i, numseqs;
  gt_lib_init();

  gt_assert(argc > 2);
  infile = argv[1];
  numseqs = atol(argv[2]);

  error = gt_error_new();
  gff3 = gt_gff3_in_stream_new_unsorted(1, &infile);
  gt_gff3_in_stream_check_id_attributes((GtGFF3InStream *)gff3);
  gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream *)gff3);

  fi1 = gt_feature_index_memory_new();
  s1 = gt_feature_out_stream_new(gff3, fi1);
  gt_node_stream_pull(s1, error);
  if(gt_error_is_set(error))
    fprintf(stderr, "error processing node stream: %s\n", gt_error_get(error));
  gt_node_stream_delete(gff3);
  gt_node_stream_delete(s1);

  fi2 = gt_feature_index_memory_new();
  seqids = gt_feature_index_get_seqids(fi1, error);
  gt_assert(gt_str_array_size(seqids) == numseqs);
  for(i = 0; i < numseqs; i++)
  {
    const char *seqid = gt_str_array_get(seqids, i);
    GtStr *seqidstr = gt_str_new_cstr(seqid);
    GtRange seqrange;
    gt_feature_index_get_orig_range_for_seqid(fi1, &seqrange, seqid, error);
    GtGenomeNode *region = gt_region_node_new(seqidstr, seqrange.start, seqrange.end);
    GtRegionNode *rn = gt_region_node_cast(region);
    gt_feature_index_add_region_node(fi2, rn, error);
    gt_genome_node_delete(region);
    gt_str_delete(seqidstr);

    GtArray *seqfeats = gt_feature_index_get_features_for_seqid(fi1, seqid, error);
    while(gt_array_size(seqfeats) > 0)
    {
      GtGenomeNode **gn = gt_array_pop(seqfeats);
      GtFeatureNode *fn = gt_feature_node_cast(*gn);
      GtRange range = gt_genome_node_get_range(*gn);
      gt_feature_index_add_feature_node(fi2, fn, error);
      printf("(fi1) %s: %s[%lu, %lu]\n", gt_feature_node_get_type(fn), seqid, range.start, range.end);
    }
    gt_array_delete(seqfeats);
  }
  gt_str_array_delete(seqids);

  fi3 = gt_feature_index_memory_new();
  s2 = gt_feature_in_stream_new(fi2);
  s3 = gt_feature_out_stream_new(s2, fi3);
  gt_node_stream_pull(s3, error);
  if(gt_error_is_set(error))
    fprintf(stderr, "error processing node stream: %s\n", gt_error_get(error));

  seqids = gt_feature_index_get_seqids(fi3, error);
  gt_assert(gt_str_array_size(seqids) == numseqs);
  for(i = 0; i < numseqs; i++)
  {
    const char *seqid = gt_str_array_get(seqids, i);
    GtArray *seqfeats = gt_feature_index_get_features_for_seqid(fi3, seqid, error);
    while(gt_array_size(seqfeats) > 0)
    {
      GtGenomeNode **gn = gt_array_pop(seqfeats);
      GtFeatureNode *fn = gt_feature_node_cast(*gn);
      GtRange range = gt_genome_node_get_range(*gn);
      printf("(fi2) %s: %s[%lu, %lu]\n", gt_feature_node_get_type(fn), seqid, range.start, range.end);
    }
    gt_array_delete(seqfeats);
  }
  gt_str_array_delete(seqids);

  gt_feature_index_delete(fi1);
  gt_feature_index_delete(fi2);
  gt_feature_index_delete(fi3);
  gt_node_stream_delete(s2);
  gt_node_stream_delete(s3);
  gt_error_delete(error);
  gt_lib_clean();
  return 0;
}