removed unused parameter in profileview-tree and updated version date

profileview-build

@@ -193,7 +193,7 @@ for query in "${PVLIB_QUERY}"/*.fa; do
     [ -e "${query}" ] || continue
     queryBase=${query##*/}
     queryName=${queryBase%.fa}
-    echo "hhblits ${HHBLITS_DBS} -i ${query} -o stdout -oa3m ${PVLIB_PREFIX}/a3m/${queryName}.a3m -ohhm ${PVLIB_PREFIX}/hhm/${queryName}.hhm -M first -qid 60 -cov 70 -id 98 -e 1e-10 -n 3 -cpu ${NTHREADS} -v 0 >/dev/null 2>&1"
+    echo "hhblits ${HHBLITS_DBS} -i ${query} -o stdout -oa3m ${PVLIB_PREFIX}/a3m/${queryName}.a3m -ohhm ${PVLIB_PREFIX}/hhm/${queryName}.hhm -M first -qid 60 -cov 70 -id 98 -e 1e-10 -n 2 -cpu ${NTHREADS} -v 0 >/dev/null 2>&1"
 done | ${PEXEC_CMD} # left it unquoted!
 
 print_status "formatting a3m files"

profileview-common

@@ -17,7 +17,7 @@
 # Common functions and definitions to be used in ProfileView
 PV_NAME="ProfileView"
 PV_VERSION='1.0'
-PV_DATE='190531'
+PV_DATE='190626'
 
 function abspath() { echo "$(cd "$(dirname "$1")"; pwd -P)/$(basename "$1")"; }
 

profileview-tree

@@ -29,7 +29,6 @@ function ctrl_c() { exit 5; }
 
 INPUT_FASTA=""
 PV_LIBPATH=""
-PV_OUTTREE=""
 PV_SEQDESC=""
 PV_OUTPREFIX="out"
 PV_TMPDIR=""
@@ -49,8 +48,6 @@ function print_usage() {
     -l, --lib <name>\tProfileView library name\n" | column -t -s $'\t'
     echo -en "\n"
     echo -en "  OTHER OPTIONS:\n
-    -o, --out-tree <name>\tOutput file which will contain the ProfileView tree\n
-                         \t(if not provided, it will be printed on the standard output)\n
     -s, --seq-desc <name>\tInput sequence descriptor file, that is a CSV file containing the follwing fileds:\n
                          \t<sequence_id>,<function_id>,<family_id>,<sequence_length>\n
     -p, --prefix <name>\tPrefix of output files (default:${PV_OUTPREFIX})\n
@@ -63,8 +60,8 @@ function print_usage() {
 
 # retrieve provided arguments
 
-opts="i:l:o:s:p:j:hV"
-longopts="input:,lib:,out-tree:,seq-desc:,prefix:,temp-dir:,max-jobs:,help,version"
+opts="i:l:s:p:j:hV"
+longopts="input:,lib:,seq-desc:,prefix:,temp-dir:,max-jobs:,help,version"
 ARGS=$(getopt -o "${opts}" -l "${longopts}" -n "${CMD_NAME}" -- "${@}")
 if [ $? -ne 0 ] || [ $# -eq 0 ]; then # the order of this tests is important!
     print_usage
@@ -83,10 +80,6 @@ while [ -n "${1}" ]; do
             shift
             PV_LIBPATH=${1}
             ;;
-        -o|--out-tree)
-            shift
-            PV_OUTTREE=${1}
-            ;;
         -s|--seq-desc)
             shift
             PV_SEQDESC=${1}