mode-0x11 forward-compatibility patch

2.0/include/pgenlib_read.cc

@@ -809,8 +809,10 @@ PglErr PgfiInitPhase1(const char* fname, const char* pgi_fname, uint32_t raw_var
   // This isn't Golang.
   char pgi_fname_buf[kPglFnamesize];
 
-  if (file_type_code != 0x20) {
-    if (unlikely(file_type_code == 0x30)) {
+  // since this branch is getting long-term support, include mode 0x11 / 0x21
+  // forward-compatibility patch
+  if ((file_type_code != 0x20) && (file_type_code != 0x21)) {
+    if (unlikely((file_type_code == 0x30) || (file_type_code == 0x31))) {
       snprintf(errstr_buf, kPglErrstrBufBlen, "Error: %s is a .pgen.pgi index file, rather than a .pgen file.\n", fname);
       return kPglRetMalformedInput;
     }
@@ -920,8 +922,7 @@ PglErr PgfiInitPhase1(const char* fname, const char* pgi_fname, uint32_t raw_var
     *pgfi_alloc_cacheline_ct_ptr = 0;
     return kPglRetSuccess;
   }
-  if (unlikely((file_type_code >= 0x11) && (file_type_code != 0x20))) {
-    // possible todo: 0x11 phase sets (unlikely before 2023, though)
+  if (unlikely((file_type_code >= 0x12) && (file_type_code != 0x20) && (file_type_code != 0x21))) {
     snprintf(errstr_buf, kPglErrstrBufBlen, "Error: Third byte of %s does not correspond to a storage mode supported by this version of pgenlib.\n", fname);
     return kPglRetNotYetSupported;
   }
@@ -1412,7 +1413,7 @@ PglErr PgfiInitPhase2(PgenHeaderCtrl header_ctrl, uint32_t allele_cts_already_lo
   const uint64_t actual_fpos = ftello(pgfip->shared_ff);
   if (actual_fpos != pgfip->var_fpos[0]) {
     // now > instead of != to allow additional information to be stored between
-    // header and first variant record
+    // header and first variant record (e.g. mode 0x11).
     if (unlikely(actual_fpos > pgfip->var_fpos[0])) {
       snprintf(errstr_buf, kPglErrstrBufBlen, "Error: Invalid .pgen%s.\n", is_pgi? ".pgi file" : " header");
       return kPglRetMalformedInput;
@@ -10053,11 +10054,12 @@ PglErr PgrValidate(PgenReader* pgr_ptr, uintptr_t* genovec_buf, char* errstr_buf
   }
   fsize = ftello(ff);
   pgrp->fp_vidx = 1;  // force fseek when loading first variant
-  // todo: modify this check when phase sets are implemented
-  const uint64_t expected_fsize = pgrp->fi.var_fpos[variant_ct];
-  if (unlikely(expected_fsize != fsize)) {
-    char* write_iter = strcpya_k(errstr_buf, "Error: .pgen header indicates that file size should be ");
-    write_iter = i64toa(expected_fsize, write_iter);
+  // todo: verify equality if no mode-0x11 footer; and if there is a footer,
+  // validate it
+  const uint64_t expected_fsize_min = pgrp->fi.var_fpos[variant_ct];
+  if (unlikely(expected_fsize_min > fsize)) {
+    char* write_iter = strcpya_k(errstr_buf, "Error: .pgen header indicates that file size should be at least ");
+    write_iter = i64toa(expected_fsize_min, write_iter);
     write_iter = strcpya_k(write_iter, " bytes, but actual file size is ");
     write_iter = i64toa(fsize, write_iter);
     strcpy_k(write_iter, " bytes.\n");

2.0/include/pgenlib_read.h

@@ -165,9 +165,9 @@ typedef struct PgenReaderMainStruct {
   uintptr_t* workspace_dosage_present;
   uintptr_t* workspace_dphase_present;
 
-  // phase set loading (mode 0x11) unimplemented for now; should be a sequence
-  // of (sample ID, [uint32_t phase set begin, set end), [set begin, set end),
-  // ...).
+  // phase set loading (footer track in mode 0x11) unimplemented for now;
+  // should be a sequence of (sample ID, [uint32_t phase set begin, set end),
+  // [set begin, set end), ...).
 } PgenReaderMain;
 
 typedef struct PgenReaderStruct {

2.0/plink2.cc

@@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.00a5.11"
 #elif defined(USE_AOCL)
   " AMD"
 #endif
-  " (xx Apr 2024)";
+  " (xx May 2024)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""