From e36e0148e2e623625b6869a8ba1fc1de93028943 Mon Sep 17 00:00:00 2001
From: Jakob Willforss <jakob.willforss@hotmail.com>
Date: Thu, 23 Jan 2025 10:38:34 +0100
Subject: [PATCH 1/2] First iteration adding d4tools create tests

---
 .../test/create/multiple-sequences-check/cmdline  |   1 +
 .../multi_reads_multi_chr.bam                     | Bin 0 -> 625 bytes
 .../multi_reads_multi_chr.bam.bai                 | Bin 0 -> 176 bytes
 .../create/multiple-sequences-check/output.txt    |  10 ++++++++++
 d4tools/test/create/single-read/cmdline           |   2 ++
 d4tools/test/create/single-read/output.txt        |   3 +++
 d4tools/test/create/single-read/single_read.bai   | Bin 0 -> 96 bytes
 d4tools/test/create/single-read/single_read.bam   | Bin 0 -> 330 bytes
 8 files changed, 16 insertions(+)
 create mode 100644 d4tools/test/create/multiple-sequences-check/cmdline
 create mode 100644 d4tools/test/create/multiple-sequences-check/multi_reads_multi_chr.bam
 create mode 100644 d4tools/test/create/multiple-sequences-check/multi_reads_multi_chr.bam.bai
 create mode 100644 d4tools/test/create/multiple-sequences-check/output.txt
 create mode 100644 d4tools/test/create/single-read/cmdline
 create mode 100644 d4tools/test/create/single-read/output.txt
 create mode 100644 d4tools/test/create/single-read/single_read.bai
 create mode 100644 d4tools/test/create/single-read/single_read.bam

diff --git a/d4tools/test/create/multiple-sequences-check/cmdline b/d4tools/test/create/multiple-sequences-check/cmdline
new file mode 100644
index 0000000..5ab05d2
--- /dev/null
+++ b/d4tools/test/create/multiple-sequences-check/cmdline
@@ -0,0 +1 @@
+${D4TOOLS} create --mapping-qual 0 multi_reads_multi_chr.bam ${OUTDIR}/multi_reads_multi_chr.d4 && ${D4TOOLS} view ${OUTDIR}/multi_reads_multi_chr.d4
\ No newline at end of file
diff --git a/d4tools/test/create/multiple-sequences-check/multi_reads_multi_chr.bam b/d4tools/test/create/multiple-sequences-check/multi_reads_multi_chr.bam
new file mode 100644
index 0000000000000000000000000000000000000000..0626202c8fd9f3c66095a7f7b3854bb6cea4685d
GIT binary patch
literal 625
zcmb2|=3rp}f&Xj_PR>jW*BN~KPjekI5O8%r==w|0$lILLS9I!{SIi+7B3AC0x?<(D
zS!|cO{=d5J(GnDHT+DXv>ACdX=hzt@eVsIC$%7o9OM7=jz0Rv#nI(JVW#f{d82P@*
zYef!!=y#ddb4bB2EM>FE^zBNWe|jg2D9$#pTiEyc<rJN5a*HprWi|?4Qf{lbzSQ(r
z&L^YvnTLEtf4$kVD^w@AcXQCPZQmj*3wNvga-`S1czTvw`*qe5vA3(!#8W4*#WK8L
zY{+N$`>i8^fgwJrlWj2rBLjmxn!joo_g*^dcgR7c?cw@~63IU@PxqHPFDN{CNz6p=
z#(|PX?w*q>%d$i|)*fVu4Y|`@crdk+Gp=d+1KBG)##24#7_PJNcDlFx`4-M=!LQ_Q
zvo%;Xgz)^f?Nq<`;#;Pf^j#leetEV8ejW3OsBO|b)22OLw*TD82?-K0TfSdhyhJW2
zDb8zE<kPIcrFQ4kPsVKckv6q*{ozkXCro;~(&ITpgzvodD?fcN4>akntj}S%6tuFa
z<>~J;t2Tz7Yf0TKdg{)p)oXqzKDr>?FhBkDwuq^p6;-3(c(|1<c^BXJWPRV2_u)~~
zKCi0z@O5I*^`Lt~KPQ>J|NQUyuKONW4>1aR{Z~HXq~RT(A6i^<(cZLS!T(F#RovGL
z=LKI)$-kK#V7i1QnenR1iE9pW?NV$PZmnkNyBnjkwXOUJkM)w2&t4MNlM=If%*=26
z-yB+UK#}>(gh{={jBmUg9GOcjKJYbs_f6e%_E9TPRKH}7zrQCiIiUx>Gy^j@je!UN
D8eARR

literal 0
HcmV?d00001

diff --git a/d4tools/test/create/multiple-sequences-check/multi_reads_multi_chr.bam.bai b/d4tools/test/create/multiple-sequences-check/multi_reads_multi_chr.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..97ac60b97717b39cc043e29ff74d2f5c7882b049
GIT binary patch
literal 176
zcmZ>A^kigWU|;}YPay^dMj*|=a05)vW`xjQlOXcw;w)fQ2m)CzvUxCb7#Ko9!VEC;
R(8bviMuAx%^AKtvk^oSQ4bK1o

literal 0
HcmV?d00001

diff --git a/d4tools/test/create/multiple-sequences-check/output.txt b/d4tools/test/create/multiple-sequences-check/output.txt
new file mode 100644
index 0000000..dcf1c67
--- /dev/null
+++ b/d4tools/test/create/multiple-sequences-check/output.txt
@@ -0,0 +1,10 @@
+chr1    0       30      1
+chr2    0       14      3
+chr2    14      15      2
+chr2    15      19      0
+chr2    19      22      1
+chr2    22      23      2
+chr2    23      25      3
+chr2    25      38      4
+chr2    38      39      3
+chr2    39      40      2
\ No newline at end of file
diff --git a/d4tools/test/create/single-read/cmdline b/d4tools/test/create/single-read/cmdline
new file mode 100644
index 0000000..2987dcb
--- /dev/null
+++ b/d4tools/test/create/single-read/cmdline
@@ -0,0 +1,2 @@
+${D4TOOLS} create --mapping-qual 0 single_read.bam ${OUTDIR}/single_read.d4 && ${D4TOOLS} view ${OUTDIR}/single_read.d4
+`
\ No newline at end of file
diff --git a/d4tools/test/create/single-read/output.txt b/d4tools/test/create/single-read/output.txt
new file mode 100644
index 0000000..4646b30
--- /dev/null
+++ b/d4tools/test/create/single-read/output.txt
@@ -0,0 +1,3 @@
+chr1    0       4       0
+chr1    4       25      1
+chr1    25      30      0
\ No newline at end of file
diff --git a/d4tools/test/create/single-read/single_read.bai b/d4tools/test/create/single-read/single_read.bai
new file mode 100644
index 0000000000000000000000000000000000000000..c6b283dd0bd709e70c26d15694811a62980b75b0
GIT binary patch
literal 96
wcmZ>A^kigYU|?VZVoxCk1`wNp;T)J`V9*0|y(U5A(ZwNZp-O=is$PgV03ss<)c^nh

literal 0
HcmV?d00001

diff --git a/d4tools/test/create/single-read/single_read.bam b/d4tools/test/create/single-read/single_read.bam
new file mode 100644
index 0000000000000000000000000000000000000000..5327d9163e56fa49f3e93594bf9a57aef851e6cb
GIT binary patch
literal 330
zcmb2|=3rp}f&Xj_PR>jWXBk}ke7O!8h_uY-7JsSuBvxVL#s!l?|1yeZtqIwsn>l;c
z6_W{JdzQ3M(mHyT$JpThn(*Tnr5O(Wowg*Xz)bz5r^vNkpYE;jt4=IZ>l8V9wou4Z
z@JF1)`xA-UpQbBq{Ntt7dS0wYf5qdPohq|e^k2+q-f~Rx68Eo)tG%XGzb5N^h+MiM
zXzRH-VXCXIY`Cp;Ir4YL?~nWY*#**VUNAbht}T@f>i%|fV~pgIdmIeM7%tSeaWd2}
ztXjNP`6<v7@@T$^XXs9BU=U+tV>5I0S9Al?foyDT{{s#HLBNz*Gm=gS95``6Va1b6
yiW*CvJi4g(L0<a9=hCzfrJY7bDFr-bV!a$?&)6BZdtBX{fW>@i24<ir1ONc1=Y#nG

literal 0
HcmV?d00001


From 853813200e985684d44f9985073d4b0366285b8a Mon Sep 17 00:00:00 2001
From: Jakob Willforss <jakob.willforss@hotmail.com>
Date: Thu, 23 Jan 2025 13:17:00 +0100
Subject: [PATCH 2/2] Make sure the tests are in order

---
 d4tools/test/create/from-bam/output.txt       | 106 +++++++++---------
 .../multiple-sequences-check/output.txt       |  24 ++--
 d4tools/test/create/single-read/cmdline       |   3 +-
 d4tools/test/create/single-read/output.txt    |   6 +-
 4 files changed, 71 insertions(+), 68 deletions(-)

diff --git a/d4tools/test/create/from-bam/output.txt b/d4tools/test/create/from-bam/output.txt
index b95787e..73af482 100644
--- a/d4tools/test/create/from-bam/output.txt
+++ b/d4tools/test/create/from-bam/output.txt
@@ -5,56 +5,56 @@
 1	10001	10002	55
 1	10002	10003	72
 1	10003	10004	93
-1	10004	10044	94
-1	10044	10046	93
-1	10046	10047	91
-1	10047	10048	90
-1	10048	10057	89
-1	10057	10059	88
-1	10059	10061	87
-1	10061	10062	86
-1	10062	10063	85
-1	10063	10064	83
-1	10064	10065	82
-1	10065	10068	78
-1	10068	10069	77
-1	10069	10071	75
-1	10071	10073	74
-1	10073	10074	71
-1	10074	10080	70
-1	10080	10081	69
-1	10081	10084	68
-1	10084	10085	67
-1	10085	10088	66
-1	10088	10089	65
-1	10089	10092	64
-1	10092	10094	62
-1	10094	10095	60
-1	10095	10102	59
-1	10102	10103	58
-1	10103	10104	54
-1	10104	10105	53
-1	10105	10106	52
-1	10106	10107	51
-1	10107	10109	49
-1	10109	10111	47
-1	10111	10113	42
-1	10113	10114	41
-1	10114	10120	36
-1	10120	10121	34
-1	10121	10126	31
-1	10126	10131	29
-1	10131	10132	28
-1	10132	10137	27
-1	10137	10138	25
-1	10138	10139	23
-1	10139	10142	21
-1	10142	10144	20
-1	10144	10146	17
-1	10146	10147	15
-1	10147	10148	14
-1	10148	10149	11
-1	10149	10150	4
-1	10150	10151	3
-1	10151	10158	1
-1	10158	20000	0
+1	10004	10043	94
+1	10043	10045	93
+1	10045	10046	91
+1	10046	10047	90
+1	10047	10056	89
+1	10056	10058	88
+1	10058	10060	87
+1	10060	10061	86
+1	10061	10062	85
+1	10062	10063	83
+1	10063	10064	82
+1	10064	10067	78
+1	10067	10068	77
+1	10068	10070	75
+1	10070	10072	74
+1	10072	10073	71
+1	10073	10079	70
+1	10079	10080	69
+1	10080	10083	68
+1	10083	10084	67
+1	10084	10087	66
+1	10087	10088	65
+1	10088	10091	64
+1	10091	10093	62
+1	10093	10094	60
+1	10094	10101	59
+1	10101	10102	58
+1	10102	10103	54
+1	10103	10104	53
+1	10104	10105	52
+1	10105	10106	51
+1	10106	10108	49
+1	10108	10110	47
+1	10110	10112	42
+1	10112	10113	41
+1	10113	10119	36
+1	10119	10120	34
+1	10120	10125	31
+1	10125	10130	29
+1	10130	10131	28
+1	10131	10136	27
+1	10136	10137	25
+1	10137	10138	23
+1	10138	10141	21
+1	10141	10143	20
+1	10143	10145	17
+1	10145	10146	15
+1	10146	10147	14
+1	10147	10148	11
+1	10148	10149	4
+1	10149	10150	3
+1	10150	10157	1
+1	10157	20000	0
diff --git a/d4tools/test/create/multiple-sequences-check/output.txt b/d4tools/test/create/multiple-sequences-check/output.txt
index dcf1c67..e8fd3ca 100644
--- a/d4tools/test/create/multiple-sequences-check/output.txt
+++ b/d4tools/test/create/multiple-sequences-check/output.txt
@@ -1,10 +1,14 @@
-chr1    0       30      1
-chr2    0       14      3
-chr2    14      15      2
-chr2    15      19      0
-chr2    19      22      1
-chr2    22      23      2
-chr2    23      25      3
-chr2    25      38      4
-chr2    38      39      3
-chr2    39      40      2
\ No newline at end of file
+chr1	0	4	2
+chr1	4	14	3
+chr1	14	18	2
+chr1	18	26	3
+chr1	26	30	2
+chr2	0	14	3
+chr2	14	15	2
+chr2	15	19	0
+chr2	19	22	1
+chr2	22	23	2
+chr2	23	25	3
+chr2	25	38	4
+chr2	38	39	3
+chr2	39	40	2
diff --git a/d4tools/test/create/single-read/cmdline b/d4tools/test/create/single-read/cmdline
index 2987dcb..aeb050f 100644
--- a/d4tools/test/create/single-read/cmdline
+++ b/d4tools/test/create/single-read/cmdline
@@ -1,2 +1 @@
-${D4TOOLS} create --mapping-qual 0 single_read.bam ${OUTDIR}/single_read.d4 && ${D4TOOLS} view ${OUTDIR}/single_read.d4
-`
\ No newline at end of file
+${D4TOOLS} create --mapping-qual 0 single_read.bam ${OUTDIR}/single_read.d4 && ${D4TOOLS} view ${OUTDIR}/single_read.d4
\ No newline at end of file
diff --git a/d4tools/test/create/single-read/output.txt b/d4tools/test/create/single-read/output.txt
index 4646b30..9afa0d4 100644
--- a/d4tools/test/create/single-read/output.txt
+++ b/d4tools/test/create/single-read/output.txt
@@ -1,3 +1,3 @@
-chr1    0       4       0
-chr1    4       25      1
-chr1    25      30      0
\ No newline at end of file
+chr1	0	4	0
+chr1	4	25	1
+chr1	25	30	0