Let normal be able to rescue tumor mapping quality.

Updated to version 0.14.1.

In install-dependencies.sh : no longer let wget use ipv4 by default, and let wget continue from previous download if possible. Updated to version 0.14.2.

Fixed a compiling error.

CmdLineArgs.cpp

@@ -980,6 +980,10 @@ CommandLineArgs::initFromArgCV(int & parsing_result_flag, int argc, const char *
         "For non-WGS: normal effective allele-fraction (FA) cannot be reduced below this times the corresponding raw FA.");
     ADD_OPTDEF2(app, lib_nonwgs_normal_add_mul_ad,
         "For non-WGS: normal cross-sample read count is increased by this multiplicative factor. ");
+    ADD_OPTDEF2(app, lib_nonwgs_normal_max_rescued_MQ,
+        "For non-WGS: additional maximum Phred-scaled increase in the mapping quality part of the variant quality by comparing the tumor with its matched normal. ");
+    ADD_OPTDEF2(app, lib_wgs_normal_max_rescued_MQ,
+        "For WGS: additional maximum Phred-scaled increase in the mapping quality part of the variant quality by comparing the tumor with its matched normal. ");
 
 // *** 14 debugging
 

CmdLineArgs.hpp

@@ -413,7 +413,9 @@ struct CommandLineArgs {
     double              lib_nonwgs_normal_full_self_rescue_fa = 0.1;
     double              lib_nonwgs_normal_min_self_rescue_fa_ratio = 0.2;
     double              lib_nonwgs_normal_add_mul_ad = 1.0;
-
+    uvc1_qual_t         lib_nonwgs_normal_max_rescued_MQ = 30;
+    uvc1_qual_t         lib_wgs_normal_max_rescued_MQ = 0;
+
 // *** 14. parameters related to debugging in vcf
     uvc1_flag_t         debug_note_flag = 0x0;
     uvc1_readpos_t      debug_warn_min_read_end_ins_cigar_oplen = 16;

install-dependencies.sh

@@ -10,7 +10,7 @@ if [ $(echo "${1}" | grep skip-bcftools | wc -l) -eq 0 ]; then
     mkdir -p "${currdir}/ext/"
     cd "${currdir}/ext/"
     if [ $(echo "${1}" | grep skip-downloading-bcftools | wc -l) -eq 0 ]; then
-        wget --inet4-only https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2
+        wget -c https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2
     fi
     tar -xvf bcftools-1.11.tar.bz2
     cd "${currdir}/ext/bcftools-1.11"
@@ -32,7 +32,7 @@ if [ $(echo "${1}" | grep skip-samtools | wc -l) -eq 0 ]; then
     mkdir -p "${currdir}/ext/"
     cd "${currdir}/ext/"
     if [ $(echo "${1}" | grep skip-downloading-samtools | wc -l) -eq 0 ]; then
-        wget --inet4-only https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
+        wget -c https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
     fi
     tar -xvf samtools-1.11.tar.bz2
     cd "${currdir}/ext/samtools-1.11"
@@ -43,7 +43,7 @@ fi
 
 if [ $(echo "${1}" | grep skip-parallel | wc -l) -eq 0 ]; then
     cd "${currdir}/ext/"
-    wget --inet4-only http://ftp.gnu.org/gnu/parallel/parallel-20201122.tar.bz2
+    wget -c http://ftp.gnu.org/gnu/parallel/parallel-20201122.tar.bz2
     tar -xvf parallel-20201122.tar.bz2
     cd "${currdir}/ext/parallel-20201122"
     ./configure

main.hpp

@@ -5220,6 +5220,8 @@ BcfFormat_symbol_calc_qual(
                 ? fmt.bMQ[a] // small
                 : (_systematicMQ_base - (uvc1_qual_t)(numstates2phred((ADP + 1.0) / (aDP + 0.5)))));
     // We may need to consider that: if an amplicon panel is designed for a target region, then there must be wet-lab protocol to deal with low mapping quality.
+    const bool is_nonWGS = does_fmt_imply_short_frag(fmt, paramset.lib_wgs_min_avg_fraglen);
+    const uvc1_qual_t normal_rescued_MQ = MIN(non_neg_minus(readlenMQcap, 60), (is_nonWGS ? paramset.lib_nonwgs_normal_max_rescued_MQ : paramset.lib_wgs_normal_max_rescued_MQ));
 
     auto systematicMQVQ1 = MIN((MAX(_systematicMQ, paramset.syserr_MQ_min) + _systematicMQVQadd), readlenMQcap);
 
@@ -5268,7 +5270,7 @@ BcfFormat_symbol_calc_qual(
              + (is_fmtADPxfr_imba ? paramset.microadjust_strand_absence_snv_penalty : 0))
             : (is_tmore_amplicon ? paramset.microadjust_dedup_absence_indel_penalty : 0));
 
-    const auto tn_syserr_q = systematicMQVQ + paramset.tn_q_inc_max;
+    const auto tn_syserr_q = systematicMQVQ + paramset.tn_q_inc_max + normal_rescued_MQ;
 
     clear_push(fmt.bMQQ, systematicMQVQ);
 

version.h

@@ -2,7 +2,7 @@
 #define version_INCLUDED
 #include <string.h>
 
-#define VERSION123 "0.14.0"
+#define VERSION123 "0.14.2"
 
 #ifndef COMMIT_VERSION
 #define COMMIT_VERSION "NotVersionControlled"