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# First field:
# INIT = initialisation, not counted in testing
# P = expected to pass
# F = expected to fail
# Second field:
# Filename of expected output
# Third onwards; command to execute. $fmt is replaced by the current file
# format, ie sam, bam or cram. $samtools is a pointer to the desired
# samtools binary. This can be useful for testing older versions.
# # Create variant formats
INIT x $samtools view -C mpileup.1.bam > mpileup.1.cram
INIT x $samtools view -C mpileup.2.bam > mpileup.2.cram
INIT x $samtools view -C mpileup.3.bam > mpileup.3.cram
INIT x $samtools index mpileup.1.cram
INIT x $samtools index mpileup.2.cram
INIT x $samtools index mpileup.3.cram
INIT x $samtools view -h mpileup.1.bam > mpileup.1.sam
INIT x $samtools view -S -b overlap50.sam > overlap50.bam
INIT x $samtools view -S -C overlap50.sam > overlap50.cram
INIT x $samtools view -S -b anomalous.sam > anomalous.bam
INIT x $samtools view -S -C anomalous.sam > anomalous.cram
INIT x $samtools view -S -b indels.sam > indels.bam
INIT x $samtools view -S -C indels.sam > indels.cram
INIT x gunzip -c expected/1.out.f3-6.gz | $awk -v OFS='\t' '{print "CHROMOSOME_I", NR, $0}' > expected/1.out
INIT x $samtools view -b -o xx#depth1.bam xx#depth1.sam
INIT x $samtools view -b -o xx#depth2.bam xx#depth2.sam
INIT x $samtools view -b -o xx#depth3.bam xx#depth3.sam
INIT x $samtools index xx#depth1.bam
INIT x $samtools index xx#depth2.bam
INIT x $samtools index xx#depth3.bam
# Nasty file corner cases
P 1.out $samtools mpileup -B -Q0 -x -f ce.fa ce#large_seq.bam
P 2.out $samtools mpileup -Q0 -x -f ce.fa ce#unmap.bam
P 3.out $samtools mpileup -Q0 -x -f ce.fa ce#unmap1.bam
P 4.out $samtools mpileup -Q0 -x -f ce.fa ce#unmap2.bam
P 5.out $samtools mpileup -Q0 -x -f c1.fa c1#clip.bam
P 6.out $samtools mpileup -Q0 -x -f c1.fa c1#pad1.bam
P 7.out $samtools mpileup -Q0 -x -f c1.fa c1#pad2.bam
# I'm not convinced this case is valid, but I also don't know if it's even
# possible to encode this data in a pileup format output.
P 8.out $samtools mpileup -Q0 -x -f c1.fa c1#pad3.bam
P 9.out $samtools mpileup -Q0 -x -f xx.fa xx#minimal.bam
P 10.out $samtools mpileup -Q0 -x -f xx.fa xx#triplet.bam
# Test basic pileup options
P 13.out $samtools mpileup -x mpileup.1.$fmt
P 14.out $samtools mpileup -x mpileup.[123].$fmt
P 15.out ls -1 mpileup.[123].$fmt > 15.list.tmp; $samtools mpileup -x -b 15.list.tmp
P 16.out $samtools mpileup -x -f mpileup.ref.fa mpileup.1.$fmt
P 17.out $samtools mpileup -x -B -f mpileup.ref.fa mpileup.1.$fmt
P 18.out $samtools mpileup -x -B -f mpileup.ref.fa mpileup.1.$fmt
P 19.out $samtools mpileup -x -f mpileup.ref.fa mpileup.1.$fmt
P 20.out $samtools mpileup -x -6 -f mpileup.ref.fa mpileup.1.$fmt
P 21.out $samtools mpileup -x -E -f mpileup.ref.fa mpileup.1.$fmt
P 22.out $samtools mpileup -x -R -f mpileup.ref.fa mpileup.1.$fmt
# -x option
P 23.out $samtools mpileup -f mpileup.ref.fa overlap50.$fmt
P 24.out $samtools mpileup -x -f mpileup.ref.fa overlap50.$fmt
# -6 for Illumina format input
P 25.out $samtools mpileup -x -6 -f mpileup.ref.fa overlapIllumina.bam
# -A for anomalous read pairs
P 26.out $samtools mpileup -x -Q0 anomalous.$fmt
P 27.out $samtools mpileup -A -x -Q0 anomalous.$fmt
# -B
P 28.out $samtools mpileup -B -x -Q1 -f mpileup.ref.fa mpileup.1.$fmt
# -q; filter by mapping quality
P 29.out $samtools mpileup -q 61 1read.bam
P 30.out $samtools mpileup -q 60 1read.bam
# -Q filter by base quality
P 31.out $samtools mpileup -Q 7 1read.bam
P 32.out $samtools mpileup -Q 8 1read.bam
# -E
P 33.out $samtools mpileup -x -f mpileup.ref.fa mpileup-E.bam
P 34.out $samtools mpileup -E -x -f mpileup.ref.fa mpileup-E.bam
# -G for excluding RG. All bar one:
P 35.out $samtools view mpileup.1.bam|sed -n 's/.*RG:Z://;s/[^A-Z0-9].*//p'|sort -u |grep -v ERR013140 > 35.rg.tmp;$samtools mpileup -G 35.rg.tmp mpileup.1.bam
# Region based options
# SAM indices don't exist (no tabix support due to header?)
# CRAM index currently fails
P 37.out $samtools mpileup -x -r 17 mpileup.1.$fmt
P 38.out $samtools mpileup -x -r 17:4000 mpileup.1.$fmt
P 39.out $samtools mpileup -x -r 17:4,000-4,010 mpileup.1.$fmt
P 40.out $samtools mpileup -l regions ce#5b.$fmt
P 41.out $samtools mpileup -l regions -r CHROMOSOME_V:40-60 ce#5b.$fmt
P 42.out $samtools mpileup -l regions -r CHROMOSOME_I:40-60 ce#5b.$fmt
# --rf and --ff
P 43.out $samtools view -h -f 16 mpileup.1.bam | $samtools mpileup -x -
P 44.out $samtools view -h mpileup.1.bam | $samtools mpileup -x --rf 0x10 -
P 45.out $samtools view -h -F 16 mpileup.1.bam | $samtools mpileup -x -
P 46.out $samtools view -h mpileup.1.bam | $samtools mpileup -x --ff 0x714 -
# -d; depth
P 47.out $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|$awk '{print $4}'
# Pileup output options; -s/O
P 76.out $samtools mpileup -Q0 -s -x -f mpileup.ref.fa mpileup.1.bam
P 77.out $samtools mpileup -Q0 -O -x -f mpileup.ref.fa mpileup.1.bam
# A more synthetic output-BP (-O) vs output-BP-5 test.
P 80.out $samtools mpileup --output-BP output-BP.sam
P 81.out $samtools mpileup --output-BP-5 output-BP.sam
# Reverse strand deletions; --reverse-del
P 78.out $samtools mpileup --reverse-del mpileup.1.bam
# Extra columns and tags; --output-extra
P 79.out $samtools mpileup -O --output-extra POS,FLAG,NM,QNAME,RG ../dat/view.001.sam
# -a and -aa. See depth.reg too
P a0.out $samtools mpileup -Q40 -r 17:1-4200 -f mpileup.ref.fa -a mpileup.1.$fmt
P a1.out $samtools mpileup -ABQ0 -a xx#depth1.sam
P a2.out $samtools mpileup -ABQ0 -a xx#depth2.sam
P a3.out $samtools mpileup -ABQ0 -a xx#depth1.sam xx#depth2.sam
P a4.out $samtools mpileup -ABQ0 -aa xx#depth1.sam
P a5.out $samtools mpileup -ABQ0 -aa xx#depth2.sam
P a6.out $samtools mpileup -ABQ0 -aa xx#depth1.sam xx#depth2.sam
# -a with regions / bed
P a8.out $samtools mpileup -ABQ0 -a -r xx:5-16 xx#depth1.bam xx#depth2.bam
P a9.out $samtools mpileup -ABQ0 -a -l xx.bed xx#depth1.bam xx#depth2.bam
P a10.out $samtools mpileup -ABQ0 -a -r xx:8-13 xx#depth1.bam xx#depth2.bam
P a11.out $samtools mpileup -ABQ0 -a -l xx.bed2 xx#depth1.bam xx#depth2.bam
# -aa with regions/bed
P a13.out $samtools mpileup -ABQ0 -a -a -r xx:5-16 xx#depth1.bam xx#depth2.bam
P a14.out $samtools mpileup -ABQ0 -a -a -l xx.bed xx#depth1.bam xx#depth2.bam
# -a with additional columns (-s and -O)
P a15.out $samtools mpileup -ABQ0 -a -s xx#depth1.sam xx#depth2.sam
P a16.out $samtools mpileup -ABQ0 -a -O xx#depth1.sam xx#depth2.sam
P a17.out $samtools mpileup -ABQ0 -a -sO xx#depth1.sam xx#depth2.sam
# Various boundary cases (see samtools#579 and #374)
# These are the same regions tested as in depth.reg.
P m5_all1.out $samtools mpileup -ABQ0 xx#depth3.bam
P m5_all2.out $samtools mpileup -ABQ0 -a xx#depth3.bam
P m5_all3.out $samtools mpileup -ABQ0 -aa xx#depth3.bam
P m5_blank.out $samtools mpileup -ABQ0 -r xy:5-6 xx#depth3.bam
P m5_blank.out $samtools mpileup -ABQ0 -a -r xy:5-6 xx#depth3.bam
P m5_xy1.out $samtools mpileup -ABQ0 -aa -r xy:5-6 xx#depth3.bam
P m5_xx1.out $samtools mpileup -ABQ0 -r xx:4-10 xx#depth3.bam
P m5_xx2.out $samtools mpileup -ABQ0 -a -r xx:4-10 xx#depth3.bam
P m5_xx2.out $samtools mpileup -ABQ0 -aa -r xx:4-10 xx#depth3.bam
P m5_blank.out $samtools mpileup -ABQ0 -r xx:9 xx#depth3.bam
P m5_blank.out $samtools mpileup -ABQ0 -a -r xx:9 xx#depth3.bam
P m5_xx3.out $samtools mpileup -ABQ0 -aa -r xx:9 xx#depth3.bam
P m5_b3.out $samtools mpileup -ABQ0 -l xx.bed3 xx#depth3.bam
P m5_b3aa.out $samtools mpileup -ABQ0 -aa -l xx.bed3 xx#depth3.bam
# Fail as -a shouldn't output xn:16-20 (it doesn't with -r)
F m5_b3a.out $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam
# -a with multiple chromosomes (see samtools#2018)
P mp_2018a.out $samtools mpileup -aB -f mp_2018.fa mp_2018.sam
P mp_2018aa.out $samtools mpileup -aaB -f mp_2018.fa mp_2018.sam
# compound I and D ops along with Pads.
P mp_D.out $samtools mpileup -ABQ0 -f mp.fa mp_D.sam
P mp_DI.out $samtools mpileup -ABQ0 -f mp.fa mp_DI.sam
P mp_I.out $samtools mpileup -ABQ0 -f mp.fa mp_I.sam
P mp_ID.out $samtools mpileup -ABQ0 -f mp.fa mp_ID.sam
P mp_N.out $samtools mpileup -ABQ0 -f mp.fa mp_N.sam
P mp_N2.out $samtools mpileup -ABQ0 -f mp.fa mp_N2.sam
P mp_P.out $samtools mpileup -ABQ0 -f mp.fa mp_P.sam
P mp_ID_rev.out $samtools mpileup -ABQ0 --reverse-del -f mp.fa mp_ID_rev.sam
# Mpileup format simplifications by omitting indels
P mp1_d.out $samtools mpileup --no-output-del mpileup.1.bam
P mp1_dd.out $samtools mpileup --no-output-del --no-output-del mpileup.1.bam
P mp1_i.out $samtools mpileup --no-output-ins mpileup.1.bam
P mp1_ii.out $samtools mpileup --no-output-ins --no-output-ins mpileup.1.bam
P mp1_iidd.out $samtools mpileup --no-output-del --no-output-del --no-output-ins --no-output-ins mpileup.1.bam
P mp1_ends.out $samtools mpileup --no-output-ends mpileup.1.bam
# Base modifications
P mp2.out $samtools mpileup -x -Q0 --output-mods mod1.sam
P mp2-noins.out $samtools mpileup -x -Q0 --output-mods --no-output-ins-mods mod1.sam
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