Emit M CIGAR operations by default instead of =/X and add --eqx option

CHANGES.md

@@ -2,27 +2,27 @@
 
 ## development version
 
-* #258: Fix compilation on MinGW. Thanks @teepean.
-* #260: Include full command line in the SAM PG header.
-* #20: Add command-line option `--m-op`. If used, emit `M` CIGAR operations
-  instead of `=` and `X`.
+* #258: Fixed compilation on MinGW. Thanks @teepean.
+* #260: Include full command line in the SAM PG header. Thanks @telmin.
+* #20: By default, emit `M` CIGAR operations instead of `=` and `X`.
+  Added option `--eqx` to use `=` and `X` as before.
 
 ## v0.9.0 (2023-03-16)
 
-* Add progress report (only shown if output is not a terminal; can be
+* Added progress report (only shown if output is not a terminal; can be
   disabled with `--no-progress`)
 * PR #250: Avoid overeager soft clipping by adding an “end bonus” to the
   alignment score if the alignment reaches the 5' or 3' end of the read.
   This is equivalent to penalizing soft-clipping and improves mapping
   accuracy, in particular for short reads, as candidate mapping sites with and
   without soft clipping are compared more fairly. Use `-L` to change the end
   bonus. (This emulates a feature found in BWA-MEM.)
-* Issue #238: Fix occasionally incorrect soft clipping.
-* PR #239: Fix an uninitialized variable that could lead to nondeterministic
+* Issue #238: Fixed occasionally incorrect soft clipping.
+* PR #239: Fixed an uninitialized variable that could lead to nondeterministic
   results.
 * Issue #137: Compute TLEN (in SAM output) correctly
-* PR #255: Add support for reading gzip-compressed reference FASTA files.
-* Issue #222: Make it possible again to build strobealign from the release
+* PR #255: Added support for reading gzip-compressed reference FASTA files.
+* Issue #222: Made it possible again to build strobealign from the release
   tarball (not only from the Git repository).
 
 ## v0.8.0 (2023-02-01)

README.md

@@ -120,6 +120,7 @@ options. Some important ones are:
   `--create-index`, see [index files](#index-files).
 * `-t N`, `--threads=N`: Use N threads. This mainly applies to the mapping step
   as the indexing step is only partially parallelized.
+* `--eqx`: Emit `=` and `X` CIGAR operations instead of `M`.
 * `-x`: Only map reads, do not do no base-level alignment. This switches the
   output format from SAM to [PAF](https://github.com/lh3/miniasm/blob/master/PAF.md).
 * `--rg-id=ID`: Add RG tag to each SAM record.

src/cmdline.cpp

@@ -26,7 +26,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     args::ValueFlag<std::string> o(parser, "PATH", "redirect output to file [stdout]", {'o'});
     args::Flag v(parser, "v", "Verbose output", {'v'});
     args::Flag no_progress(parser, "no-progress", "Disable progress report (enabled by default if output is a terminal)", {"no-progress"});
-    args::Flag cigar_m(parser, "cigar-m", "Use CIGAR M instead of =/X", {"m-op"});
+    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 U(parser, "U", "Suppress output of unmapped reads", {'U'});
     args::Flag interleaved(parser, "interleaved", "Interleaved input", {"interleaved"});
@@ -89,7 +89,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     if (o) { opt.output_file_name = args::get(o); opt.write_to_stdout = false; }
     if (v) { opt.verbose = true; }
     if (no_progress) { opt.show_progress = false; }
-    if (cigar_m) { opt.cigar_eqx = false; }
+    if (eqx) { opt.cigar_eqx = true; }
     if (x) { opt.is_sam_out = false; }
     if (U) { opt.output_unmapped = false; }
     if (rgid) { opt.read_group_id = args::get(rgid); }

src/cmdline.hpp

@@ -14,7 +14,7 @@ struct CommandLineOptions {
     bool write_to_stdout { true };
     bool verbose { false };
     bool show_progress { true };
-    bool cigar_eqx { true };
+    bool cigar_eqx { false };
     std::string read_group_id { "" };
     std::vector<std::string> read_group_fields;
     std::string logfile_name { "" };

tests/run.sh

@@ -21,18 +21,18 @@ if strobealign -G > /dev/null 2> /dev/null; then false; fi
 strobealign -h > /dev/null
 
 # Single-end SAM
-strobealign --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 --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
 diff tests/phix.se.sam phix.se.sam
 rm phix.se.sam
 
 # Single-end SAM, M CIGAR operators
-strobealign --m-op tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.m.sam
+strobealign tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > 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 --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 --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
 diff tests/phix.pe.sam phix.pe.sam
 rm phix.pe.sam