prefix header print

cobilab · Oct 20, 2022 · aa6b8d6 · aa6b8d6
1 parent cfa90d3
commit aa6b8d6
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Showing 3 changed files with 23 additions and 7 deletions.
diff --git a/pipelines/Simulation.sh b/pipelines/Simulation.sh
@@ -1,13 +1,13 @@
 #!/bin/bash
 #
-ITERATIONS=20000;
-RATE=0.00005;
+ITERATIONS=10000;
+RATE=0.0001;
 #
 rm -f ALL.fa;
 #
 printf "\n" > DIV;
 #
-gto_genomic_gen_random_dna -n 2000 -s 7 \
+gto_genomic_gen_random_dna -n 5000 -s 7 \
 | gto_fasta_from_seq -n "Synthetic DNA" > ORIGINAL.fa
 #
 cp ORIGINAL.fa IN.fa

diff --git a/src/defs.h b/src/defs.h
@@ -99,6 +99,7 @@ typedef int8_t   I8;
 #define DEF_NC_LEVEL           11
 #define DEF_NC_MIN_THREADS     1
 #define DEF_NC_MAX_THREADS     999999
+#define HEADERS_PREFIX_SIZE    50
 
 #define DEF_NCD_HELP           0
 #define DEF_NCD_FORCE          0

diff --git a/src/nc.c b/src/nc.c
@@ -495,7 +495,10 @@ void NormalizedCompression(NC_PARAMETERS *MAP)
 
   if(P->verbose) fprintf(stderr, "[>] Compressing %s ...\n", !P->dna ? 
 		 "DNA" : "Aminoacids");
-
+
+  char identifier_prefix[FA->nReads+1][HEADERS_PREFIX_SIZE+1];
+  uint32_t idx_header = 0;
+
   while((k = fread(buffer, 1, BUFFER_SIZE, F)))
     for(idx = 0 ; idx < k ; ++idx)
       {
@@ -512,17 +515,29 @@ void NormalizedCompression(NC_PARAMETERS *MAP)
         continue;
         }
       if(sym == '\n' && header == 1)
-        { header = 0; nSymbols = 0; continue; }
+        { 
+	header = 0; 
+	nSymbols = 0; 
+	identifier_prefix[idx_reads-1][idx_header] = '\0';
+	idx_header = 0;
+       	continue; 
+	}
       if(sym == '\n') continue;
-      if(header == 1) continue;
+      if(header == 1)
+        {
+	if(idx_header < HEADERS_PREFIX_SIZE)
+	  identifier_prefix[idx_reads-1][idx_header++] = sym;
+	continue;
+        }
       SEQ[nSymbols++] = sym;
       }
 
   if(!P->dna) vr[idx_reads-1] = CompressTargetRead   (SEQ, nSymbols);
   else        vr[idx_reads-1] = CompressTargetReadAA (SEQ, nSymbols);
 
   for(idx_reads = 0 ; idx_reads < FA->nReads ; ++idx_reads)
-    fprintf(stdout, "%"PRIu64"\t%lf\n", idx_reads+1, vr[idx_reads]);
+    fprintf(stdout, "%"PRIu64"\t%lf\t%s\n", idx_reads+1, vr[idx_reads], 
+    identifier_prefix[idx_reads]);
 
   fclose(F);