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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
##############################################
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/vcf2structure.sh-3-
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/vcf2structure.sh:4:out_name=`echo $1 | sed -e 's/.vcf//g'`
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/vcf2structure.sh-5-#extract genotypes
##############################################
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md-72-
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md:73:`ls ${discofile}.fa > ${discofile}.fof `
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md-74-
##############################################
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md-77-
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md:78:`./quick_hierarchical_clustering ${discofile}.txt > ${discofile}.cluster`
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md-79-
##############################################
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md-85-
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md:86:**NB**: Then the `${discofile}_with_clusters.vcf` can be simply sorted to put
discosnp-4.4.4/discoSnpRAD/post-processing_scripts/README.md-87-together variants from each cluster.
##############################################
discosnp-4.4.4/discoSnpRAD/run_discoSnpRad.sh-489-#######################################
discosnp-4.4.4/discoSnpRAD/run_discoSnpRad.sh:490:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/discoSnpRAD/run_discoSnpRad.sh-491-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/scripts/jenkins/tool-discosnp-release-debian.sh-70- cd ${TOOL_GIT_HOME}
discosnp-4.4.4/scripts/jenkins/tool-discosnp-release-debian.sh:71: DOES_TAG_EXIST=`git tag -l | grep "^${BRANCH_TO_BUILD}$"`
discosnp-4.4.4/scripts/jenkins/tool-discosnp-release-debian.sh-72- if [ -z ${DOES_TAG_EXIST} ] ; then
##############################################
discosnp-4.4.4/scripts/k3000/run.sh-34-echo "${green}${bold} ### EXPLOITATION OF PHASING INFORMATION OBTAINED FROM DISCOSNP${reset}"
discosnp-4.4.4/scripts/k3000/run.sh:35:echo "${green} ### Input phased_allele_file: `sha1sum ${phased_allele_file}`${reset}"
discosnp-4.4.4/scripts/k3000/run.sh:36:echo "${green} ### Input disco_fa_file: `sha1sum ${disco_fa_file}`${reset}"
discosnp-4.4.4/scripts/k3000/run.sh-37-echo "${green} ### Input read_set_id: ${read_set_id}${reset}"
##############################################
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-68-
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:69:for p in `seq 1 $num_pop`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-70- do
##############################################
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-75- #nb all mut
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:76: nb_line_all=`grep "." -c ERASEME_pos_mut_random_pop"$p"`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-77- #nb_mut_pop_specific
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:78: nb_shared_all=`echo $(($nb_line_all/100*$perc_sha ))`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-79- head -n +"$nb_shared_all" ERASEME_pos_mut_random_pop"$p" > ERASEME_pos_mut_random_shared_allpop"$p"
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:80: nb_spe=`echo $(($nb_shared_all+1 ))`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-81- tail -n +"$nb_spe" ERASEME_pos_mut_random_pop"$p" > ERASEME_pos_mut_random_to_separate_by_pop"$p"
##############################################
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-83-
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:84: for i in `seq 1 $num_sample`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-85- do
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:86: nb_line=`grep "." -c ERASEME_pos_mut_random_to_separate_by_pop"$p"`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:87: nb_shared=`echo $(($nb_line/100*$perc_spe ))`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-88- #selection rondomly 80% of the mutations for each of the 20 samples
##############################################
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-95- #homozygote and heterozygote mutations
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:96: nb_line2=`grep "." -c ERASEME_pos_mut_random_shared_pop"$p"_s"$i"`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh:97: nb_homo=`echo $(($nb_line2/100*$perc_H ))`
discosnp-4.4.4/scripts/simulations/multiple_samples_simulator.sh-98- #homo mutations
##############################################
discosnp-4.4.4/debian/createmanpages-4-
discosnp-4.4.4/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
discosnp-4.4.4/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
##############################################
discosnp-4.4.4/debian/patches/2to3.patch-239-
discosnp-4.4.4/debian/patches/2to3.patch:240: for p in `seq 1 $num_pop`
discosnp-4.4.4/debian/patches/2to3.patch-241- do
##############################################
discosnp-4.4.4/debian/patches/2to3.patch-246- sort -R ERASEME_pos_mut_pop"$p" > ERASEME_pos_mut_random_pop"$p"
discosnp-4.4.4/debian/patches/2to3.patch:247:@@ -90,7 +90,7 @@ for p in `seq 1 $num_pop`
discosnp-4.4.4/debian/patches/2to3.patch-248- #homozygotes mutations
##############################################
discosnp-4.4.4/debian/patches/2to3.patch-254- #homozygote and heterozygote mutations
discosnp-4.4.4/debian/patches/2to3.patch:255: nb_line2=`grep "." -c ERASEME_pos_mut_random_shared_pop"$p"_s"$i"`
discosnp-4.4.4/debian/patches/2to3.patch:256:@@ -99,7 +99,7 @@ for p in `seq 1 $num_pop`
discosnp-4.4.4/debian/patches/2to3.patch-257- head -n +"$nb_homo" ERASEME_pos_mut_random_shared_pop"$p"_s"$i" > ERASEME_pos_mut_random_shared_pop"$p"_s"$i"_homo
##############################################
discosnp-4.4.4/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
discosnp-4.4.4/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
discosnp-4.4.4/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
##############################################
discosnp-4.4.4/.pc/path_to_readme_file_names.patch/run_discoSnp++.sh-419-#######################################
discosnp-4.4.4/.pc/path_to_readme_file_names.patch/run_discoSnp++.sh:420:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/.pc/path_to_readme_file_names.patch/run_discoSnp++.sh-421-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-68-
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:69:for p in `seq 1 $num_pop`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-70- do
##############################################
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-75- #nb all mut
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:76: nb_line_all=`grep "." -c ERASEME_pos_mut_random_pop"$p"`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-77- #nb_mut_pop_specific
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:78: nb_shared_all=`echo $(($nb_line_all/100*$perc_sha ))`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-79- head -n +"$nb_shared_all" ERASEME_pos_mut_random_pop"$p" > ERASEME_pos_mut_random_shared_allpop"$p"
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:80: nb_spe=`echo $(($nb_shared_all+1 ))`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-81- tail -n +"$nb_spe" ERASEME_pos_mut_random_pop"$p" > ERASEME_pos_mut_random_to_separate_by_pop"$p"
##############################################
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-83-
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:84: for i in `seq 1 $num_sample`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-85- do
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:86: nb_line=`grep "." -c ERASEME_pos_mut_random_to_separate_by_pop"$p"`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:87: nb_shared=`echo $(($nb_line/100*$perc_spe ))`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-88- #selection rondomly 80% of the mutations for each of the 20 samples
##############################################
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-95- #homozygote and heterozygote mutations
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:96: nb_line2=`grep "." -c ERASEME_pos_mut_random_shared_pop"$p"_s"$i"`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh:97: nb_homo=`echo $(($nb_line2/100*$perc_H ))`
discosnp-4.4.4/.pc/2to3.patch/scripts/simulations/multiple_samples_simulator.sh-98- #homo mutations
##############################################
discosnp-4.4.4/.pc/2to3.patch/scripts/k3000/run.sh-34-echo "${green}${bold} ### EXPLOITATION OF PHASING INFORMATION OBTAINED FROM DISCOSNP${reset}"
discosnp-4.4.4/.pc/2to3.patch/scripts/k3000/run.sh:35:echo "${green} ### Input phased_allele_file: `sha1sum ${phased_allele_file}`${reset}"
discosnp-4.4.4/.pc/2to3.patch/scripts/k3000/run.sh:36:echo "${green} ### Input disco_fa_file: `sha1sum ${disco_fa_file}`${reset}"
discosnp-4.4.4/.pc/2to3.patch/scripts/k3000/run.sh-37-echo "${green} ### Input read_set_id: ${read_set_id}${reset}"
##############################################
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md-72-
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md:73:`ls ${discofile}.fa > ${discofile}.fof `
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md-74-
##############################################
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md-77-
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md:78:`./quick_hierarchical_clustering ${discofile}.txt > ${discofile}.cluster`
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md-79-
##############################################
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md-85-
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md:86:**NB**: Then the `${discofile}_with_clusters.vcf` can be simply sorted to put
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/post-processing_scripts/README.md-87-together variants from each cluster.
##############################################
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/run_discoSnpRad.sh-489-#######################################
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/run_discoSnpRad.sh:490:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/.pc/2to3.patch/discoSnpRAD/run_discoSnpRad.sh-491-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++.sh-420-#######################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++.sh:421:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++.sh-422-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_storagefile.sh-304-#######################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_storagefile.sh:305:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_storagefile.sh-306-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-439-#######################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh:440:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-441-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-536- ab_index_size="${#array[@]}"
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh:537: for line in `cat ${read_sets}_${kissprefix}_removemeplease`; do
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-538- min_abundance="${array[$i]}"
##############################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-542- fi
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh:543: i=`expr $i + 1`
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-544- dskCmd="${dsk_build_dir}/dsk -file ${line} -abundance-min ${min_abundance} -abundance-max 2147483647 -solidity-kind sum -kmer-size $k -out ${prefix_trash}_trashme_${i}.h5"
##############################################
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-581-
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh:582: for file in `ls ${prefix_trash}_trashme_[0-9]*.fa.gz`;
discosnp-4.4.4/.pc/2to3.patch/run_discoSnp++_ML.sh-583- do
##############################################
discosnp-4.4.4/run_discoSnp++.sh-420-#######################################
discosnp-4.4.4/run_discoSnp++.sh:421:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/run_discoSnp++.sh-422-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/run_discoSnp++_storagefile.sh-304-#######################################
discosnp-4.4.4/run_discoSnp++_storagefile.sh:305:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/run_discoSnp++_storagefile.sh-306-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/run_discoSnp++_ML.sh-439-#######################################
discosnp-4.4.4/run_discoSnp++_ML.sh:440:c_filename=`echo ${c} | tr ',' '_'`
discosnp-4.4.4/run_discoSnp++_ML.sh-441-if [ $C -ne $max_C ]
##############################################
discosnp-4.4.4/run_discoSnp++_ML.sh-536- ab_index_size="${#array[@]}"
discosnp-4.4.4/run_discoSnp++_ML.sh:537: for line in `cat ${read_sets}_${kissprefix}_removemeplease`; do
discosnp-4.4.4/run_discoSnp++_ML.sh-538- min_abundance="${array[$i]}"
##############################################
discosnp-4.4.4/run_discoSnp++_ML.sh-542- fi
discosnp-4.4.4/run_discoSnp++_ML.sh:543: i=`expr $i + 1`
discosnp-4.4.4/run_discoSnp++_ML.sh-544- dskCmd="${dsk_build_dir}/dsk -file ${line} -abundance-min ${min_abundance} -abundance-max 2147483647 -solidity-kind sum -kmer-size $k -out ${prefix_trash}_trashme_${i}.h5"
##############################################
discosnp-4.4.4/run_discoSnp++_ML.sh-581-
discosnp-4.4.4/run_discoSnp++_ML.sh:582: for file in `ls ${prefix_trash}_trashme_[0-9]*.fa.gz`;
discosnp-4.4.4/run_discoSnp++_ML.sh-583- do