extend samtool -F filter to remove supplementary reads before subsamp…

…ling (for realignment)

add informational messages showing reads_count and calculated frac to log (stderr output)

data/vtlib/subsample.json

@@ -42,7 +42,7 @@
 		"use_STDOUT": true,
 		"cmd":[
 			"bash -c '",
-			{"subst_constructor":{"vals":["tmfs=\"", {"subst":"tag_metrics_files", "required":true}, "\""],"postproc":{"op":"concat","pad":""}}}, "; if [ ! -z \"${tmfs}\" ]; then for tag_metrics_file in ${tmfs}; do reads_count=`jq", {"subst":"jqkey", "ifnull":{"subst_constructor":{"vals":["'\"'\"'.reads_count.\"", {"subst":"s2_tag_index", "required":true}, "\"'\"'\"'"],"postproc":{"op":"concat","pad":""}}}}, "${tag_metrics_file}`; reads_count=`echo ${reads_count} | tr -cd [:digit:]`; reads_count_total=$((${reads_count_total}+${reads_count})); done; if [[ $reads_count_total -eq 0 ]]; then reads_count_total=1; fi; frac=`echo \"10000/${reads_count_total}\" | bc -l`; fi;",
+			{"subst_constructor":{"vals":["tmfs=\"", {"subst":"tag_metrics_files", "required":true}, "\""],"postproc":{"op":"concat","pad":""}}}, "; if [ ! -z \"${tmfs}\" ]; then for tag_metrics_file in ${tmfs}; do reads_count=`jq", {"subst":"jqkey", "ifnull":{"subst_constructor":{"vals":["'\"'\"'.reads_count.\"", {"subst":"s2_tag_index", "required":true}, "\"'\"'\"'"],"postproc":{"op":"concat","pad":""}}}}, "${tag_metrics_file}`; reads_count=`echo ${reads_count} | tr -cd [:digit:]`; reads_count_total=$((${reads_count_total}+${reads_count}));  >&2 printf \"reads_count_total: %d\\n\" ${reads_count_total}; done; if [[ $reads_count_total -eq 0 ]]; then reads_count_total=1; fi; frac=`echo \"10000/${reads_count_total}\" | bc -l`; fi; >&2 printf \"frac: %0.2f\\n\" ${frac};",
 			"if [ ! -z $frac ]; then",
 				"samtools",
 				"view",
@@ -60,7 +60,7 @@
 		"use_STDOUT": true,
 		"cmd":[ "samtools",
 			"fastq",
-			"-F", "0x200",
+			"-F", "0xB00",
 			{"select":"s2_se_pe", "default":"pe", "select_range":[1], "cases":{
 				"pe":["-1", {"port":"ss_fq1", "direction":"out"},"-2", {"port":"ss_fq2", "direction":"out"}],
 				"se":["-0", {"port":"ss_fq1", "direction":"out"}]