=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-26-__shunit_oldShellFlags="$-" sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:27:for _shunit_shellFlag in `echo "${__SHUNIT_SHELL_FLAGS}" |sed 's/\(.\)/\1 /g'` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-28-do ############################################## sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-260- # see if condition is an integer, i.e. a return value sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:261: _su_match=`expr "${_su_condition}" : '\([0-9]*\)'` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-262- if [ -z "${_su_condition}" ]; then ############################################## sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-323- # see if condition is an integer, i.e. a return value sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:324: _su_match=`expr "${_su_condition}" : '\([0-9]*\)'` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-325- if [ -z "${_su_condition}" ]; then ############################################## sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-630- # add 128 to signal and exit sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:631: exit `expr ${signal} + 128` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-632- fi ############################################## sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-704- _su__date=`date '+%Y%m%d%H%M%S'` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:705: _su__random=`expr ${_su__date} / $$` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-706- fi ############################################## sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-734-{ sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:735: __shunit_testsPassed=`expr ${__shunit_testsPassed} + 1` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:736: __shunit_testsTotal=`expr ${__shunit_testsTotal} + 1` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-737-} ############################################## sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-742- sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:743: __shunit_testsFailed=`expr ${__shunit_testsFailed} + 1` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:744: __shunit_testsTotal=`expr ${__shunit_testsTotal} + 1` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-745- echo "${__SHUNIT_ASSERT_MSG_PREFIX}${_su__msg}" >&2 ############################################## sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-774-if [ -z "${__shunit_suite}" ]; then sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2:775: funcs=`grep "^[ \t]*test[A-Za-z0-9_]* *()" $0 |sed 's/[^A-Za-z0-9_]//g'` sambamba-0.7.1/contrib/shunit2-2.0.3/shunit2-776- for func in ${funcs}; do ############################################## sambamba-0.7.1/deb/makepackage.rb-152- Dir.chdir '..' sambamba-0.7.1/deb/makepackage.rb:153: `fakeroot dpkg-deb --build #{$rootdir}` sambamba-0.7.1/deb/makepackage.rb-154-end ############################################## sambamba-0.7.1/scripts/dropbox.sh-2-for i in "$@"; do sambamba-0.7.1/scripts/dropbox.sh:3: CONTENT_LENGTH=`ls -la "$i" | awk '{ print $5}'` sambamba-0.7.1/scripts/dropbox.sh-4- curl --request PUT --header "Content-Length: "${CONTENT_LENGTH}"" --header "Content-Type: multipart/mixed" --data-binary "@"$i"" "https://api-content.dropbox.com/1/files_put/sandbox/$i?access_token="${ACCESS_TOKEN}"" ############################################## sambamba-0.7.1/scripts/bioconda_push.sh-5-python3 bioconda_yaml_gen.py > $UPDATED_RECIPE sambamba-0.7.1/scripts/bioconda_push.sh:6:VERSION=`grep version $UPDATED_RECIPE | cut -d\' -f2` sambamba-0.7.1/scripts/bioconda_push.sh-7- ############################################## sambamba-0.7.1/test/test_suite.sh-34- $sambamba $opts index $nsortedbam sambamba-0.7.1/test/test_suite.sh:35: assertEquals "aabb4fb319497dec1069028dd354eeda" `$sambamba $opts view -f unpack $nsortedbam |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh:36: assertEquals "68e19d0f1092e1f0429ba07b418d1d9f" `$sambamba $opts view -f unpack $sortedbam |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh-37-} ############################################## sambamba-0.7.1/test/test_suite.sh-46- # should be same as sorted bam sambamba-0.7.1/test/test_suite.sh:47: assertEquals "6e226f6acc8466115600d4de52ca8944" `$sambamba $opts view -f unpack $outfn |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh-48- outfn=$outdir/subsample2.bam ############################################## sambamba-0.7.1/test/test_suite.sh-50- assertEquals 0 $? sambamba-0.7.1/test/test_suite.sh:51: assertEquals "4092fb75c87cde6efc47ff0a4dc443fb" `$sambamba $opts view -f unpack $outfn |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh-52-} ############################################## sambamba-0.7.1/test/test_suite.sh-58- $sambamba $opts view -t2 $nsortedbam > $outfn sambamba-0.7.1/test/test_suite.sh:59: assertEquals "3270" `wc -l < $outfn` sambamba-0.7.1/test/test_suite.sh-60- cat $outfn | cut -f1 | LC_ALL=C sort -c ############################################## sambamba-0.7.1/test/test_suite.sh-70- # check sorted with cat output/ex1_header.sorted2.bam.sam |awk '{print $3 " " $4}'|less sambamba-0.7.1/test/test_suite.sh:71: assertEquals "d92c51b9e067590d7d5a18a0bdbbe0cc" `$sambamba $opts view -f unpack $outfn |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh-72-} ############################################## sambamba-0.7.1/test/test_suite.sh-78- $sambamba $opts view -t2 $outfn > $outfn.sam sambamba-0.7.1/test/test_suite.sh:79: assertEquals "2d9af987d7aeaf3a38396870a2f30dca" `$sambamba $opts view -f unpack $outfn |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh-80-} ############################################## sambamba-0.7.1/test/test_suite.sh-85- assertEquals 0 $? sambamba-0.7.1/test/test_suite.sh:86: assertEquals "8a0b62e1ac85185c31cf66126c876217" `$sambamba $opts view -f unpack $outfn |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh-87-} ############################################## sambamba-0.7.1/test/test_suite.sh-92- assertEquals 0 $? sambamba-0.7.1/test/test_suite.sh:93: assertEquals "8a0b62e1ac85185c31cf66126c876217" `$sambamba $opts view -f unpack $outfn |$md5sum|cut -c 1-32` sambamba-0.7.1/test/test_suite.sh-94-} ############################################## sambamba-0.7.1/test/test_suite.sh-112-testView() { sambamba-0.7.1/test/test_suite.sh:113: assertEquals "1806" `$sambamba $opts view -c $sortedbam chr2` sambamba-0.7.1/test/test_suite.sh:114: assertEquals "1464" `$sambamba $opts view -c $sortedbam chr1` sambamba-0.7.1/test/test_suite.sh:115: assertEquals "0" `$sambamba $opts view -c $sortedbam '*'` sambamba-0.7.1/test/test_suite.sh-116-} ############################################## sambamba-0.7.1/test/test_suite.sh-133- $sambamba $opts sort -m 50M $outdir/empty.bam -o $outdir/empty2.bam 2>/dev/null sambamba-0.7.1/test/test_suite.sh:134: assertEquals "0" `$sambamba $opts view -c $outdir/empty2.bam` sambamba-0.7.1/test/test_suite.sh-135-} ############################################## sambamba-0.7.1/test/test_suite.sh-139- $sambamba $opts markdup $outdir/empty.bam $outdir/empty.dedup.bam 2>/dev/null sambamba-0.7.1/test/test_suite.sh:140: assertEquals "0" `$sambamba $opts view -c $outdir/empty.dedup.bam` sambamba-0.7.1/test/test_suite.sh-141-} ############################################## sambamba-0.7.1/debian/patches/2to3.patch-69-+python3 bioconda_yaml_gen.py > $UPDATED_RECIPE sambamba-0.7.1/debian/patches/2to3.patch:70: VERSION=`grep version $UPDATED_RECIPE | cut -d\' -f2` sambamba-0.7.1/debian/patches/2to3.patch-71- ############################################## sambamba-0.7.1/.pc/2to3.patch/scripts/bioconda_push.sh-5-python bioconda_yaml_gen.py > $UPDATED_RECIPE sambamba-0.7.1/.pc/2to3.patch/scripts/bioconda_push.sh:6:VERSION=`grep version $UPDATED_RECIPE | cut -d\' -f2` sambamba-0.7.1/.pc/2to3.patch/scripts/bioconda_push.sh-7-