diff --git a/src/JARVIS3.sh b/src/JARVIS3.sh index 7de7af8..63356c0 100755 --- 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 deleted file mode 100755 index cc2dcdf..0000000 Binary files a/src/extra/MergeFastaStreams and /dev/null differ diff --git a/src/extra/MergeFastqStreams b/src/extra/MergeFastqStreams deleted file mode 100755 index c170139..0000000 Binary files a/src/extra/MergeFastqStreams and /dev/null differ diff --git a/src/extra/MergeFastqStreams.c b/src/extra/MergeFastqStreams.c index e3efef6..8f0061c 100644 --- a/src/extra/MergeFastqStreams.c +++ b/src/extra/MergeFastqStreams.c @@ -2,6 +2,7 @@ #include #include #include +#include // 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 deleted file mode 100755 index 5cf00d3..0000000 Binary files a/src/extra/SplitFastaStreams and /dev/null differ diff --git a/src/extra/SplitFastqStreams b/src/extra/SplitFastqStreams deleted file mode 100755 index 6ccff75..0000000 Binary files a/src/extra/SplitFastqStreams and /dev/null differ diff --git a/src/extra/XScoreC b/src/extra/XScoreC index 7521e47..1ed00f5 100755 Binary files a/src/extra/XScoreC and b/src/extra/XScoreC differ diff --git a/src/extra/XScoreD b/src/extra/XScoreD index e93445b..fa45c89 100755 Binary files a/src/extra/XScoreD and b/src/extra/XScoreD differ diff --git a/src/extra/bbb b/src/extra/bbb index c98d0e1..78cb8b4 100755 Binary files a/src/extra/bbb and b/src/extra/bbb differ diff --git a/src/extra/bzip2 b/src/extra/bzip2 index d7172f1..1a5f3f0 100755 Binary files a/src/extra/bzip2 and b/src/extra/bzip2 differ diff --git a/src/extra/levels.h b/src/extra/levels.h index b64d381..062f68d 100644 --- 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 "