fix bug w long read

cobilab · Oct 2, 2023 · 0d40fd6 · 0d40fd6
1 parent 5a592a5
commit 0d40fd6
Show file tree

Hide file tree

Showing 11 changed files with 11 additions and 9 deletions.
diff --git a/src/JARVIS3.sh b/src/JARVIS3.sh
@@ -15,7 +15,7 @@ THREADS="8";
 SHOW_MENU () {
   echo " -------------------------------------------------------";
   echo "                                                        ";
-  echo " JARVIS3, v3.4. High reference-free compression of DNA  ";
+  echo " JARVIS3, v3.5. High reference-free compression of DNA  ";
   echo "                sequences, FASTA data, and FASTQ data.  ";
   echo "                                                        ";
   echo " Program options ---------------------------------------";
@@ -80,7 +80,7 @@ SHOW_HEADER () {
   echo " [JARVIS3 :: DNA, FASTA, and FASTQ Extensions]          ";
   echo "                                                        ";
   echo " Release year: 2024,                                    ";
-  echo " Version: 3.4                                           ";
+  echo " Version: 3.5                                           ";
   echo " Author: D. Pratas                                      ";
   echo " Language: Bash / C                                     ";
   echo " License: GPL v3                                        ";
@@ -103,7 +103,7 @@ MERGE_DNA () {
   #
   mapfile -t FILES < .DEC_F_JV3;
   #
-  D_NAMES="";
+  NAMES="";
   IDX_T=1;
   IDX_POS=1;
   #
@@ -366,7 +366,7 @@ if [[ "$DECOMPRESS" -eq "0" ]];
     SPLIT_DNA "DNA.JV3" "$BLOCK" "$THREADS" "$LEVEL" &
     ./bzip2 -f N.JV3 &
     ./bbb cfm10q HEADERS.JV3 HEADERS.JV3.bbb &
-    ./XScoreC -l 2 QUALITIES.JV3 1> .tmp_report_out_xc 2> .tmp_report_err_xc &
+    ./XScoreC -l 1 QUALITIES.JV3 1> .tmp_report_out_xc 2> .tmp_report_err_xc &
     wait
     tar -cvf $INPUT.tar DNA.JV3.tar N.JV3.bz2 HEADERS.JV3.bbb QUALITIES.JV3.co 1> .rep_main_info;
     echo "Done!";

diff --git a/src/extra/MergeFastaStreams b/src/extra/MergeFastaStreams
diff --git a/src/extra/MergeFastqStreams b/src/extra/MergeFastqStreams
diff --git a/src/extra/MergeFastqStreams.c b/src/extra/MergeFastqStreams.c
@@ -2,6 +2,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <ctype.h>
+#include <stdint.h>
 
 // This application merges four channels of information: 
 //        * HEADERS;
@@ -35,7 +36,8 @@ int main(int argc, char *argv[]){
     return 1;
     }
 
-  unsigned idx = 0, idx2 = 0, n, max = 10000;
+  // FIXME: IF READ LARGER THAN 2000000 PROBLEMS WILL OCCUR 
+  uint64_t idx = 0, idx2 = 0, n, max = 1000000;
   int qual_str[max+1];
   int n_str   [max+1];
 
@@ -68,13 +70,13 @@ int main(int argc, char *argv[]){
       if(n_str[n] == 'a'){
 	c = fgetc(DNA);
         if(c == EOF) break;
-	else fprintf(stdout, "%c", c);
+	else fprintf(stdout, "%c", c); // WRITE DNA
         }
-      else fprintf(stdout, "N");
+      else fprintf(stdout, "N"); // WRITE N
       }
 
     fprintf(stdout, "\n+\n");
-    for(n = 0 ; n <= idx ; ++n)
+    for(n = 0 ; n <= idx ; ++n) // WRITE QUALS
       fprintf(stdout, "%c", qual_str[n]);
     }
 

diff --git a/src/extra/SplitFastaStreams b/src/extra/SplitFastaStreams
diff --git a/src/extra/SplitFastqStreams b/src/extra/SplitFastqStreams
diff --git a/src/extra/XScoreC b/src/extra/XScoreC
diff --git a/src/extra/XScoreD b/src/extra/XScoreD
diff --git a/src/extra/bbb b/src/extra/bbb
diff --git a/src/extra/bzip2 b/src/extra/bzip2
diff --git a/src/extra/levels.h b/src/extra/levels.h
@@ -5,7 +5,7 @@
 
 // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 //
-#define LEVEL_1 " 1: -tm 1:1:0.95/0:0:0 -tm 4:100:0.2/0:0:0 "
+#define LEVEL_1 " 1: -tm 3:1:0.2/0:0:0 "
 #define LEVEL_2 " 2: -tm 1:1:0.95/0:0:0 -tm 4:200:0.2/0:0:0 "
 #define LEVEL_3 " 3: -tm 2:10:0.95/0:0:0 -tm 4:200:0.2/0:0:0 "
 #define LEVEL_4 " 4: -tm 2:10:0.95/0:0:0 -tm 6:500:0.2/0:0:0 "