Added tests for FASTA files

Author: pmelsted

.gitignore

@@ -2,7 +2,9 @@
 *~
 bamhash_checksum_bam
 bamhash_checksum_fastq
+bamhash_checksum_fasta
 test/r*.fastq
+test/r*.fasta
 test/r*.bam
 test/r*.md5sum
 test/ecoliMG1655.fa*

test/Makefile

@@ -1,16 +1,18 @@
 
 
 FASTQBIN=../bamhash_checksum_fastq
+FASTABIN=../bamhash_checksum_fasta
 BAMBIN=../bamhash_checksum_bam
 WGSIM=wgsim
+SEQTK=seqtk
 
 REF=ecoliMG1655.fa
 
 .PHONY: FORCE clean reallyclean
 
 
 #r.namesorted.fastq.md5sum FORCE
-r: r.sorted.bam.md5sum r.unsorted.bam.md5sum r.fastq.md5sum r.namesorted.bam.md5sum r.single.sorted.bam.md5sum r.single.unsorted.bam.md5sum r.single.fastq.md5sum r.single.namesorted.bam.md5sum r.repeat.unsorted.bam.md5sum r.repeat.sorted.bam.md5sum r.repeat.mixed.bam.md5sum r.repeat.fastq.md5sum FORCE
+r: r.sorted.bam.md5sum r.unsorted.bam.md5sum r.fastq.md5sum r.namesorted.bam.md5sum r.single.sorted.bam.md5sum r.single.unsorted.bam.md5sum r.single.fastq.md5sum r.single.namesorted.bam.md5sum r.repeat.unsorted.bam.md5sum r.repeat.sorted.bam.md5sum r.repeat.mixed.bam.md5sum r.repeat.fastq.md5sum r.fasta.md5sum r.single.noqual.bam.md5sum FORCE
 	for x in r*.md5sum; do echo $$x $$(cat $$x); done
 
 # retrieve ref from internet if not already available
@@ -23,14 +25,13 @@ ${REF}.bwt: ${REF}
 
 r1.fastq: ${REF}.bwt
 	${WGSIM} -N 10 ${REF} r1.fastq r2.fastq
-	#sed '1~4N; s/\/1//' r1.tmp.fastq > r1.fastq
-	#sed '1~4N; s/\/2//' r2.tmp.fastq > r2.fastq
-	#rm r1.tmp.fastq r2.tmp.fastq
 
 
 r2.fastq: r1.fastq
 	#noop
 
+r1.fasta: r1.fastq
+	${SEQTK} seq -a r1.fastq | sed 's/\/[1-2]$$//' > r1.fasta
 
 r.unsorted.bam: r1.fastq r2.fastq
 	bwa mem ${REF} r1.fastq r2.fastq | samtools view -bSh - > r.unsorted.bam
@@ -81,6 +82,9 @@ r.single.namesorted.bam.md5sum: r.single.namesorted.bam FORCE
 r.single.unsorted.bam.md5sum: r.single.unsorted.bam FORCE
 	${BAMBIN} r.single.unsorted.bam > r.single.unsorted.bam.md5sum
 
+r.single.noqual.bam.md5sum: r.single.sorted.bam FORCE
+	${BAMBIN} -Q r.single.sorted.bam > r.single.noqual.bam.md5sum
+
 r.repeat.unsorted.bam.md5sum: r.unsorted.bam FORCE
 	${BAMBIN} r.unsorted.bam r.unsorted.bam > r.repeat.unsorted.bam.md5sum
 
@@ -104,6 +108,10 @@ r.repeat.fastq.md5sum: r1.fastq r2.fastq FORCE
 	${FASTQBIN} r1.fastq r2.fastq r1.fastq r2.fastq > r.repeat.fastq.md5sum
 
 
+r.fasta.md5sum: r1.fasta FORCE
+	${FASTABIN} r1.fasta > r.fasta.md5sum
+
+
 FORCE: