Add --no-PG option for not outputting the @pg SAM header

This is useful for our tests where we need output to be consistent even if
the version number of the program changes.

The name of the option is chosen to be consistent with "samtools view".

src/cmdline.cpp

@@ -28,6 +28,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     args::Flag no_progress(parser, "no-progress", "Disable progress report (enabled by default if output is a terminal)", {"no-progress"});
     args::Flag eqx(parser, "eqx", "Emit =/X instead of M CIGAR operations", {"eqx"});
     args::Flag x(parser, "x", "Only map reads, no base level alignment (produces PAF file)", {'x'});
+    args::Flag no_pg(parser, "no-PG", "Do not output PG header", {"no-PG"});
     args::Flag U(parser, "U", "Suppress output of unmapped reads", {'U'});
     args::Flag interleaved(parser, "interleaved", "Interleaved input", {"interleaved"});
     args::ValueFlag<std::string> rgid(parser, "ID", "Read group ID", {"rg-id"});
@@ -91,6 +92,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     if (v) { opt.verbose = true; }
     if (details) { opt.details = true; }
     if (no_progress) { opt.show_progress = false; }
+    if (no_pg) { opt.pg_header = false; }
     if (eqx) { opt.cigar_eqx = true; }
     if (x) { opt.is_sam_out = false; }
     if (U) { opt.output_unmapped = false; }

src/cmdline.hpp

@@ -22,6 +22,7 @@ struct CommandLineOptions {
     bool only_gen_index { false };
     bool use_index { false };
     bool is_sam_out { true };
+    bool pg_header { true };
     bool output_unmapped { true };
     int max_secondary { 0 };
 

src/main.cpp

@@ -33,7 +33,11 @@ static Logger& logger = Logger::get();
 /*
  * Return formatted SAM header as a string
  */
-std::string sam_header(const References& references, const std::string& read_group_id, const std::vector<std::string>& read_group_fields, const std::string& cmd_line) {
+std::string sam_header(
+    const References& references,
+    const std::string& read_group_id,
+    const std::vector<std::string>& read_group_fields
+) {
     std::stringstream out;
     out << "@HD\tVN:1.6\tSO:unsorted\n";
     for (size_t i = 0; i < references.size(); ++i) {
@@ -46,6 +50,11 @@ std::string sam_header(const References& references, const std::string& read_gro
         }
         out << '\n';
     }
+    return out.str();
+}
+
+std::string pg_header(const std::string& cmd_line) {
+    std::stringstream out;
     out << "@PG\tID:strobealign\tPN:strobealign\tVN:" << version_string() << "\tCL:" << cmd_line << std::endl;
     return out.str();
 }
@@ -280,7 +289,10 @@ int run_strobealign(int argc, char **argv) {
             cmd_line << argv[i] << " ";
         }
 
-        out << sam_header(references, opt.read_group_id, opt.read_group_fields, cmd_line.str());
+        out << sam_header(references, opt.read_group_id, opt.read_group_fields);
+        if (opt.pg_header) {
+            out << pg_header(cmd_line.str());
+        }
     }
 
     std::vector<AlignmentStatistics> log_stats_vec(opt.n_threads);

tests/run.sh

@@ -26,18 +26,18 @@ ${strobealign} -h > /dev/null
 samtools --version > /dev/null
 
 # Single-end SAM
-${strobealign} --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library -v tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.sam
+${strobealign} --no-PG --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library -v tests/phix.fasta tests/phix.1.fastq > phix.se.sam
 diff tests/phix.se.sam phix.se.sam
 rm phix.se.sam
 
 # Single-end SAM, M CIGAR operators
-${strobealign} tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.m.sam
+${strobealign} --no-PG tests/phix.fasta tests/phix.1.fastq > phix.se.m.sam
 if samtools view phix.se.m.sam | cut -f6 | grep -q '[X=]'; then false; fi
 
 rm phix.se.m.sam
 
 # Paired-end SAM
-${strobealign} --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq | grep -v '^@PG' > phix.pe.sam
+${strobealign} --no-PG --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq > phix.pe.sam
 diff tests/phix.pe.sam phix.pe.sam
 rm phix.pe.sam
 
@@ -57,9 +57,9 @@ diff tests/phix.pe.paf phix.pe.paf
 rm phix.pe.paf
 
 # Build a separate index
-${strobealign} -r 150 tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > without-sti.sam
+${strobealign} --no-PG -r 150 tests/phix.fasta tests/phix.1.fastq > without-sti.sam
 ${strobealign} -r 150 -i tests/phix.fasta
-${strobealign} -r 150 --use-index tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-sti.sam
+${strobealign} --no-PG -r 150 --use-index tests/phix.fasta tests/phix.1.fastq > with-sti.sam
 diff without-sti.sam with-sti.sam
 rm without-sti.sam with-sti.sam
 
@@ -73,17 +73,17 @@ ${strobealign} --details tests/phix.fasta tests/phix.1.fastq 2> /dev/null | samt
 # Secondary alignments
 
 # No secondary alignments on phix
-${strobealign} tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > no-secondary.sam
-${strobealign} -N 5 tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-secondary.sam
+${strobealign} --no-PG tests/phix.fasta tests/phix.1.fastq > no-secondary.sam
+${strobealign} --no-PG -N 5 tests/phix.fasta tests/phix.1.fastq > with-secondary.sam
 test $(samtools view -f 0x100 -c with-secondary.sam) -eq 0
 rm no-secondary.sam with-secondary.sam
 
 # Secondary alignments for repeated phiX
 cp tests/phix.fasta repeated-phix.fasta
 echo ">repeated_NC_001422" >> repeated-phix.fasta
 sed 1d tests/phix.fasta >> repeated-phix.fasta
-${strobealign} repeated-phix.fasta tests/phix.1.fastq | grep -v '^@PG' > no-secondary.sam
-${strobealign} -N 5 repeated-phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-secondary.sam
+${strobealign} --no-PG repeated-phix.fasta tests/phix.1.fastq > no-secondary.sam
+${strobealign} --no-PG -N 5 repeated-phix.fasta tests/phix.1.fastq > with-secondary.sam
 test $(samtools view -f 0x100 -c with-secondary.sam) -gt 0
 
 # Removing secondary alignments gives same result as not producing them in the first place