fixing stitch and no fastq

neat/read_simulator/utils/generate_reads.py

@@ -268,10 +268,14 @@ def generate_reads(
         )
 
         read_1.mutations = find_applicable_mutations(read_1, contig_variants)
+        if options.produce_fastq:
+            fastq_handle = ofw.files_to_write[ofw.fq1]
+        else:
+            fastq_handle = None
         read_1.finalize_read_and_write(
             error_model,
             qual_model,
-            ofw.files_to_write[ofw.fq1],
+            fastq_handle,
             options.quality_offset,
             options.produce_fastq,
             options.rng
@@ -303,10 +307,14 @@ def generate_reads(
 
             read_2.mutations = find_applicable_mutations(read_2, contig_variants)
 
+            if options.produce_fastq:
+                fastq_handle = ofw.files_to_write[ofw.fq2]
+            else:
+                fastq_handle = None
             read_2.finalize_read_and_write(
                 error_model,
                 qual_model,
-                ofw.files_to_write[ofw.fq2],
+                fastq_handle,
                 options.quality_offset,
                 options.produce_fastq,
                 options.rng

neat/read_simulator/utils/output_file_writer.py

@@ -80,6 +80,7 @@ def __init__(self,
         self.vcf_header = vcf_header
         self.bam_header = bam_header
         self.vcf_format = vcf_format
+        self.tmp_dir = options.temp_dir_path
 
         file_handles: dict[Path, Any] = {}
 

neat/read_simulator/utils/split_inputs.py

@@ -4,7 +4,7 @@
 
 import shutil
 import sys
-import gzip
+import resource
 from pathlib import Path
 from textwrap import wrap
 from typing import Iterator
@@ -83,6 +83,12 @@ def main(options: Options, reference_index: dict) -> tuple[dict, int]:
                 idx += 1
                 written += 1
 
+    # soft_limit, hard_limit = resource.getrlimit(resource.RLIMIT_NOFILE)
+    # # plus one for the final file to write
+    # if hard_limit > written + 1 >= soft_limit:
+    #     resource.setrlimit(resource.RLIMIT_NOFILE, (written + 1, hard_limit))
+    # elif written + 1 >= hard_limit:
+    #     raise ValueError("Too many files for psyam merge to work successfully, increase Size parameter and try again.")
     # Report success via the logger instead of printing to stderr
     _LOG.info(f"Generated {written} FASTAs in {options.splits_dir}")
     return split_fasta_dict, written

neat/read_simulator/utils/stitch_outputs.py

@@ -1,7 +1,7 @@
 """
 Stitch NEAT split‑run outputs into one dataset.
 """
-
+import resource
 import shutil
 import pysam
 from pathlib import Path
@@ -30,11 +30,17 @@ def merge_vcfs(vcfs: List[Path], ofw: OutputFileWriter) -> None:
                 if not line.startswith("#"):
                     dest.write(line)
 
-def merge_bam(bam_files: List[Path], ofw: OutputFileWriter, threads: int) -> None:
-    unsorted = ofw.bam.with_suffix(".unsorted.bam")
-    pysam.merge("--no-PG", "-@", str(threads), "-f", str(unsorted), *map(str, bam_files))
-    pysam.sort("-@", str(threads), "-o", str(ofw.bam), str(unsorted))
-    unsorted.unlink(missing_ok=True)
+def merge_bam(bam_files: List[Path], ofw: OutputFileWriter, threads: int):
+    merged_file = ofw.tmp_dir / "temp_merged.bam"
+    intermediate_files = []
+    # Note 1000 is abritrary. May need to be a user parameter/adjustable/a function
+    for i in range(0, len(bam_files), 500):
+        temp_file = str(ofw.tmp_dir / f"temp_merged_{i}.bam")
+        pysam.merge("--no-PG", "-f", temp_file, *map(str, bam_files[i:i+500]))
+        intermediate_files.append(temp_file)
+    pysam.merge("--no-PG", "-f", str(merged_file), *intermediate_files)
+    pysam.sort("-@", str(threads), "-m", "1G", "-o", str(ofw.bam), str(merged_file))
+    merged_file.unlink(missing_ok=True)
 
 def main(
         ofw: OutputFileWriter,