Use an asterisk for empty SEQ fields in SAM

Otherwise (when the field is left empty), samtools view converts it to "*" in the output, which makes testing harder because of spurious differences.
ksahlin · Nov 17, 2023 · fd798bd · fd798bd
1 parent 8c74210
commit fd798bd
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Showing 4 changed files with 13 additions and 8 deletions.
diff --git a/src/sam.cpp b/src/sam.cpp
@@ -83,7 +83,7 @@ void Sam::add_unmapped(const KSeq& record, uint16_t flags) {
     sam_string.append("\t");
     sam_string.append(std::to_string(flags));
     sam_string.append("\t*\t0\t" SAM_UNMAPPED_MAPQ_STRING "\t*\t*\t0\t0\t");
-    sam_string.append(record.seq);
+    append_seq(record.seq);
     append_qual(record.qual);
     append_rg_and_newline();
 }
@@ -105,7 +105,7 @@ void Sam::add_unmapped_mate(const KSeq& record, uint16_t flags, const std::strin
     sam_string.append("\t");
     sam_string.append(std::to_string(mate_pos + 1));
     sam_string.append("\t0\t");
-    sam_string.append(record.seq);
+    append_seq(record.seq);
     append_qual(record.qual);
     append_rg_and_newline();
 }
@@ -176,11 +176,11 @@ void Sam::add_record(
     sam_string.append("\t");
 
     if (flags & SECONDARY) {
-        sam_string.append("*");
+        append_seq("");
     } else if (flags & REVERSE) {
-        sam_string.append(query_sequence_rc);
+        append_seq(query_sequence_rc);
     } else {
-        sam_string.append(query_sequence);
+        append_seq(query_sequence);
     }
 
     if (!(flags & UNMAP)) {

diff --git a/src/sam.hpp b/src/sam.hpp
@@ -86,6 +86,11 @@ class Sam {
 
 private:
     void add_record(const std::string& query_name, uint16_t flags, const std::string& reference_name, uint32_t pos, uint8_t mapq, const Cigar& cigar, const std::string& mate_reference_name, uint32_t mate_pos, int32_t template_len, const std::string& query_sequence, const std::string& query_sequence_rc, const std::string& qual, int ed, int aln_score, const Details& details);
+
+    void append_seq(const std::string& seq) {
+        sam_string.append(seq.empty() ? "*" : seq);
+    }
+
     void append_qual(const std::string& qual) {
         sam_string.append("\t");
         sam_string.append(qual.empty() ? "*" : qual);

diff --git a/tests/phix.pe.sam b/tests/phix.pe.sam
@@ -89,5 +89,5 @@ rescuable.43	83	NC_001422.1	3137	60	120S14=1X4=1X9=1X4=1X4=1X9=1X4=1X4=1X4=1X9=1
 rescuable.43	163	NC_001422.1	2955	60	1X177=1X122=	=	3137	362	NTTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGT	#8BCCGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEFGGGCFGGGGFGGGGGGGGGGGGGGGGFGGGFFCGGGFGGGGGGGGGGGGGGGFGGDEG>C9:FCFFDFGCFGGGGGGFFGFFFFF4AAFFFFFFFFFFFFFBEFFFFFE=@@8C@3>BF=4=>;?6?@F@;E<CE@FF<E3.<?37);?E?94<>:<A>BFF?F6?F?)))<?FFF###	NM:i:2	AS:i:602	RG:Z:1
 not.rescuable	89	NC_001422.1	3017	60	116=1X183=1X	=	3017	0	CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN	6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8#	NM:i:2	AS:i:602	RG:Z:1
 not.rescuable	165	NC_001422.1	3017	0	*	=	3017	0	GGTTTCGCAGCACCTGCACGGCGCCGTTTCTAGGACGTACATACCGGACAAGAGTATATCCGCGATGGACGGGTGATCCATGTAGGAAGTCTAGT	GGGGGFFFFFFFFEEB@F29?3>EGGGGG8#GGGGGFAFEFFFFB=6>EEEGGGGBGGGGGGG;<;7EF;@EEC9CEFF??6?EF<@EDFFF###	RG:Z:1
-empty	77	*	0	0	*	*	0	0		*	RG:Z:1
-empty	141	*	0	0	*	*	0	0		*	RG:Z:1
+empty	77	*	0	0	*	*	0	0	*	*	RG:Z:1
+empty	141	*	0	0	*	*	0	0	*	*	RG:Z:1
diff --git a/tests/phix.se.sam b/tests/phix.se.sam
@@ -45,4 +45,4 @@ unmappable.41	4	*	0	0	*	*	0	0	TGCATGCAGTACGTGCTCGCCGTAGGTTGTGGCTCATTCCTGCAACACGT
 rescuable.42	16	NC_001422.1	3017	60	116=1X183=1X	*	0	0	CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN	6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8#	NM:i:2	AS:i:602	RG:Z:1
 rescuable.43	4	*	0	0	*	*	0	0	ATAAGATCAGAAAATACAGCAGCAAAATAAACACGAGTATACTTTACTTTATCAGAGGCAAACTTACCACAAAGTACAACAAAATAAAGCAACTTATCAGAAACGACAGAAGTGCAAGCCAGCAAAGTACATTCAAGAAGACCTTAACCAACTTTAGCCAAAGCAACAGAAACAAAACTAAGGACAGCCTAATCAAGGTTAGGAAAATTAAAGCCATGAAAGGCAAATTTAATACAAGCAACACCAATGCATACAATATTATTATAGGTAACAAGAACATAACCTAGAATACCACAGGAG	8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGFGGGGGGGGGGGGGGD7?>DFGGGGFGFGGFGFGFFFFFFFFFFFFFEFCEFFFFEF;+,26CEFDF;@<@EFFFFBFFFBF?BFFFFF6	RG:Z:1
 not.rescuable	16	NC_001422.1	3017	60	116=1X183=1X	*	0	0	CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN	6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8#	NM:i:2	AS:i:602	RG:Z:1
-empty	4	*	0	0	*	*	0	0		*	RG:Z:1
+empty	4	*	0	0	*	*	0	0	*	*	RG:Z:1