From 0d40fd6577043963e22cc7a9d1945b34804feb30 Mon Sep 17 00:00:00 2001 From: pratas <6882743+pratas@users.noreply.github.com> Date: Mon, 2 Oct 2023 15:18:27 +0100 Subject: [PATCH] fix bug w long read --- src/JARVIS3.sh | 8 ++++---- src/extra/MergeFastaStreams | Bin 16240 -> 0 bytes src/extra/MergeFastqStreams | Bin 16240 -> 0 bytes src/extra/MergeFastqStreams.c | 10 ++++++---- src/extra/SplitFastaStreams | Bin 16240 -> 0 bytes src/extra/SplitFastqStreams | Bin 16184 -> 0 bytes src/extra/XScoreC | Bin 59768 -> 59768 bytes src/extra/XScoreD | Bin 59704 -> 59704 bytes src/extra/bbb | Bin 58304 -> 58304 bytes src/extra/bzip2 | Bin 144880 -> 144880 bytes src/extra/levels.h | 2 +- 11 files changed, 11 insertions(+), 9 deletions(-) delete mode 100755 src/extra/MergeFastaStreams delete mode 100755 src/extra/MergeFastqStreams delete mode 100755 src/extra/SplitFastaStreams delete mode 100755 src/extra/SplitFastqStreams 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 cc2dcdf896441532ef5960ee75c4cf0e85e54561..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16240 zcmeHOZ)_aJ6`woX;6QSA0wGQaWJ75iD8Be#QbRG^IsUUoPGS;=rYh;??Ax=ixhACH`+R~+mAFHYHnTz^A!RuJc~yZ3iFUCJ z$93X*aT)Y#8~d*gDe9$8yc()1 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