added --reduced option to bam2*/sam2* wrapper scripts

bedops · Jul 17, 2017 · 3800d8d · 3800d8d
1 parent 611da80
commit 3800d8d
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Showing 4 changed files with 36 additions and 4 deletions.
diff --git a/applications/bed/conversion/src/wrappers/bam2bed b/applications/bed/conversion/src/wrappers/bam2bed
@@ -37,14 +37,15 @@ all_reads=false
 keep_header=false
 split=false
 split_with_deletions=false
+reduced=false
 
 help()
 {
     ${cmd} --help-bam
     exit $1
 }
 
-optspec=":r:m:dhaksS-:"
+optspec=":r:m:dhaksSR-:"
 while getopts "$optspec" optchar; do
     case "${optchar}" in
         -)
@@ -98,6 +99,9 @@ while getopts "$optspec" optchar; do
                 split-with-deletions)
                     split_with_deletions=true
                     ;;
+                reduced)
+                    reduced=true
+                    ;;
                 *)
                     help 1
                     #if [ "$OPTERR" = 1 ] && [ "${optspec:0:1}" != ":" ]; then echo "Unknown option --${OPTARG}" >&2; fi
@@ -129,6 +133,9 @@ while getopts "$optspec" optchar; do
         S)
             split_with_deletions=true
             ;;
+        R)
+            reduced=true
+            ;;
         *)
             help 1
             #if [ "$OPTERR" != 1 ] || [ "${optspec:0:1}" = ":" ]; then echo "Non-option argument: '-${OPTARG}'" >&2; fi
@@ -152,5 +159,6 @@ if [ "${all_reads}" = true ]; then options="${options} --all-reads"; fi
 if [ "${keep_header}" = true ]; then options="${options} --keep-header"; fi
 if [ "${split}" = true ]; then options="${options} --split"; fi
 if [ "${split_with_deletions}" = true ]; then options="${options} --split-with-deletions"; fi
+if [ "${reduced}" = true ]; then options="${options} --reduced"; fi
 
 ${cmd} ${options} - <&0
diff --git a/applications/bed/conversion/src/wrappers/bam2starch b/applications/bed/conversion/src/wrappers/bam2starch
@@ -41,14 +41,15 @@ all_reads=false
 keep_header=false
 split=false
 split_with_deletions=false
+reduced=false
 
 help()
 {
     ${cmd} --help-bam
     exit $1
 }
 
-optspec=":e:zgr:m:dhaksS-:"
+optspec=":e:zgr:m:dhaksSR-:"
 while getopts "$optspec" optchar; do
     case "${optchar}" in
         -)
@@ -118,6 +119,9 @@ while getopts "$optspec" optchar; do
                 split-with-deletions)
                     split_with_deletions=true
                     ;;
+                reduced)
+                    reduced=true
+                    ;;
                 *)
                     help 1
                     #if [ "$OPTERR" = 1 ] && [ "${optspec:0:1}" != ":" ]; then echo "Unknown option --${OPTARG}" >&2; fi
@@ -159,6 +163,9 @@ while getopts "$optspec" optchar; do
         S)
             split_with_deletions=true
             ;;
+        R)
+            reduced=true
+            ;;
         *)
             help 1
             #if [ "$OPTERR" != 1 ] || [ "${optspec:0:1}" = ":" ]; then echo "Non-option argument: '-${OPTARG}'" >&2; fi
@@ -185,5 +192,6 @@ if [ "${all_reads}" = true ]; then options="${options} --all-reads"; fi
 if [ "${keep_header}" = true ]; then options="${options} --keep-header"; fi
 if [ "${split}" = true ]; then options="${options} --split"; fi
 if [ "${split_with_deletions}" = true ]; then options="${options} --split-with-deletions"; fi
+if [ "${reduced}" = true ]; then options="${options} --reduced"; fi
 
 ${cmd} ${options} - <&0
diff --git a/applications/bed/conversion/src/wrappers/sam2bed b/applications/bed/conversion/src/wrappers/sam2bed
@@ -37,14 +37,15 @@ all_reads=false
 keep_header=false
 split=false
 split_with_deletions=false
+reduced=false
 
 help()
 {
     ${cmd} --help-sam
     exit $1
 }
 
-optspec=":r:m:dhaksS-:"
+optspec=":r:m:dhaksSR-:"
 while getopts "$optspec" optchar; do
     case "${optchar}" in
         -)
@@ -98,6 +99,9 @@ while getopts "$optspec" optchar; do
                 split-with-deletions)
                     split_with_deletions=true
                     ;;
+                reduced)
+                    reduced=true
+                    ;;
                 *)
                     help 1
                     #if [ "$OPTERR" = 1 ] && [ "${optspec:0:1}" != ":" ]; then echo "Unknown option --${OPTARG}" >&2; fi
@@ -129,6 +133,9 @@ while getopts "$optspec" optchar; do
         S)
             split_with_deletions=true
             ;;
+        R)
+            reduced=true
+            ;;
         *)
             help 1
             #if [ "$OPTERR" != 1 ] || [ "${optspec:0:1}" = ":" ]; then echo "Non-option argument: '-${OPTARG}'" >&2; fi
@@ -152,5 +159,6 @@ if [ "${all_reads}" = true ]; then options="${options} --all-reads"; fi
 if [ "${keep_header}" = true ]; then options="${options} --keep-header"; fi
 if [ "${split}" = true ]; then options="${options} --split"; fi
 if [ "${split_with_deletions}" = true ]; then options="${options} --split-with-deletions"; fi
+if [ "${reduced}" = true ]; then options="${options} --reduced"; fi
 
 ${cmd} ${options} - <&0
diff --git a/applications/bed/conversion/src/wrappers/sam2starch b/applications/bed/conversion/src/wrappers/sam2starch
@@ -41,14 +41,15 @@ all_reads=false
 keep_header=false
 split=false
 split_with_deletions=false
+reduced=false
 
 help()
 {
     ${cmd} --help-sam
     exit $1
 }
 
-optspec=":e:zgr:m:dhaks-:"
+optspec=":e:zgr:m:dhaksSR-:"
 while getopts "$optspec" optchar; do
     case "${optchar}" in
         -)
@@ -118,6 +119,9 @@ while getopts "$optspec" optchar; do
                 split-with-deletions)
                     split_with_deletions=true
                     ;;
+                reduced)
+                    reduced=true
+                    ;;
                 *)
                     help 1
                     #if [ "$OPTERR" = 1 ] && [ "${optspec:0:1}" != ":" ]; then echo "Unknown option --${OPTARG}" >&2; fi
@@ -159,6 +163,9 @@ while getopts "$optspec" optchar; do
         S)
             split_with_deletions=true
             ;;
+        R)
+            reduced=true
+            ;;
         *)
             help 1
             #if [ "$OPTERR" != 1 ] || [ "${optspec:0:1}" = ":" ]; then echo "Non-option argument: '-${OPTARG}'" >&2; fi
@@ -185,5 +192,6 @@ if [ "${all_reads}" = true ]; then options="${options} --all-reads"; fi
 if [ "${keep_header}" = true ]; then options="${options} --keep-header"; fi
 if [ "${split}" = true ]; then options="${options} --split"; fi
 if [ "${split_with_deletions}" = true ]; then options="${options} --split-with-deletions"; fi
+if [ "${reduced}" = true ]; then options="${options} --reduced"; fi
 
 ${cmd} ${options} - <&0