Handle windows newlines on input files

src/libprimer3.cc

@@ -7207,6 +7207,10 @@ p3_read_line(FILE *file)
 
     if ((n = strchr(p, '\n')) != NULL) {
       *n = '\0';
+      n--;
+      if (*n == '\r') {
+        *n = '\0';
+      }
       return s;
     }
 

test/p3test.pl

@@ -314,6 +314,8 @@ ()
 			'primer_new_tasks',
 			'primer_new_tasks_formatted',
 
+			'primer_windows_newlines',
+
 			'primer_must_overlap_point',
 			'primer_overlap_junction',
 

test/primer_windows_newlines_input

@@ -0,0 +1,52 @@
+PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT=1
+PRIMER_TM_FORMULA=1
+PRIMER_SALT_CORRECTIONS=1
+PRIMER_SALT_DIVALENT=1.5
+PRIMER_MAX_SELF_ANY=12
+PRIMER_PAIR_MAX_COMPL_ANY=12
+PRIMER_MAX_POLY_X=100
+PRIMER_MAX_SELF_END=8
+PRIMER_PAIR_MAX_COMPL_END=8
+P3_FILE_FLAG=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_TASK=pick_pcr_primers
+PRIMER_DNTP_CONC=0.0
+SEQUENCE_ID=pcr_primers
+SEQUENCE_TEMPLATE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
+SEQUENCE_TARGET=21,122
+=
+SEQUENCE_ID=pcr_primers_and_io
+PRIMER_TASK=pick_pcr_primers_and_hyb_PROBE
+SEQUENCE_TEMPLATE=NATCCANGCTGTTTCACACTTACGGAAATGGANGACTNCCCATAGCTNCTGGGCTNTTATCCAAAAAACATTCTCTNNNTGNTGCTTATTGGCNTCTCNAAGTGTGCNNACTTCATGGGCCTACACANAATTGNNCANGGGCTTAGCGTGCGTGGGGTCCCTNGGTAACATNGGCATCTCTGCACTTCNNGGTNNCCTTCCTTCTNACCAAGGGGTATCTGGNTGCCAGTGGCTTTTCTCCAACAGGAANGGGGGTATGTGCATTNGCAGACATCAATGANCATGAGAGATATNAATAGG
+=
+SEQUENCE_ID=left_only
+PRIMER_TASK=pick_left_only
+SEQUENCE_TARGET=100,20
+SEQUENCE_TEMPLATE=GNATCTGCACCCTGTAAACCCTGGCTCCTGCCTCTCCGGGACACCCCACTGAGGTCAGCACACCCTGCAGGTTTAGAAGGGGTGTCTGGGTGCATTTGGTGACACCGCAGGCAGAGGGGGGACNCCACAGCCAGCTCTGCCCGCGGATGCCACGTCCATTTGCTTCAGCAGGATC
+=
+SEQUENCE_ID=right_only
+PRIMER_TASK=PICK_right_only
+SEQUENCE_TARGET=90,10
+SEQUENCE_TEMPLATE=GANCAATGCANGTAATGANGTTGGCANAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACTTCCAAAACGCAAAGCACGCTCCCGATC
+=
+SEQUENCE_ID=hyb_probe_only
+PRIMER_TASK=pick_HYB_probe_ONly
+SEQUENCE_INTERNAL_EXCLUDED_REGION=90,20
+SEQUENCE_TEMPLATE=GCATCTGCACCCTGTAAACCCTGGCTCCTGCCTCTCCGGGACACCCCACTGAGGTCAGCACACCCTGCAGGTTTAGAAGGGGTGTCTGGGTGCATTTGGTGACACCGCAGGCAGAGGGGGGACNCCACAGCCAGCTCTGCCCGCGGATGCCACGTCCATTTGCTTCAGCAGGATC
+=
+SEQUENCE_ID=left_only
+PRIMER_MIN_SIZE=20
+PRIMER_MAX_SIZE=20
+PRIMER_TASK=pick_left_only
+SEQUENCE_TEMPLATE=TTAGAAGGGGTGTCTGGGTG
+=
+SEQUENCE_ID=right_only
+PRIMER_TASK=pick_left_only
+SEQUENCE_TEMPLATE=TTAGAAGGGGTGTCTGGGTG
+=
+SEQUENCE_ID=hyb_probe_only
+PRIMER_INTERNAL_MIN_SIZE=20
+PRIMER_INTERNAL_MAX_SIZE=20
+PRIMER_TASK=pick_left_only
+SEQUENCE_TEMPLATE=TTAGAAGGGGTGTCTGGGTG
+=